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Influx of NASL talent
Prior to the start of the season, the NPSL became a beneficiary of the uncertainty surrounding the 2018 North American Soccer League season, since three NASL clubs decided to field many of their Division II-quality players in NPSL matches. First, Jacksonville Armada FC owner Robert Palmer announced that the team would compete in NPSL in 2018, replacing the club's reserve side, Jacksonville Armada U-23. Palmer said the roster would include five or six players from the NASL squad and that the players would be using the NPSL games as a preseason training opportunity until the then expected start of the NASL season in August.

The following day, Miami FC CEO Sean Flynn announced the formation of a reserve squad, Miami FC 2, which entered NPSL as an expansion team. Flynn said that he created Miami FC 2 to provide Miami FC's players with live match action instead of being confined to training as they waited for the start of the NASL season.

On February 27, 2018, the NASL announced that it had cancelled its 2018 season; it also announced that three of its teams, Miami FC, Jacksonville Armada FC and the New York Cosmos would be fielding teams in NPSL. Shortly thereafter, Carlos Mendes was hired as head coach of the New York Cosmos B, the organization's reserve side which had competed in NPSL since 2015. Within days the Cosmos B signed Danny Szetela, Chris Wingert, Bljedi Bardic, Jonathan Borrajo, Alexis Velela and Wojciech Wojcik.

NPSL at the U.S. Open Cup
The United States Soccer Federation's Open Cup Committee initially allocated 19 berths in the 2018 U.S. Open Cup to NPSL teams. NPSL expansion club El Farolito had made it through the open division qualifying process. However, tournament rules require that a participating team remain a playing member in good standing of the same league from the date of the open division entry deadline through the date of the U.S. Open Cup Final. By jumping from the San Francisco Soccer Football League to the NPSL, El Farolito had disqualified itself.

As a Division II league, NASL was entitiled to send all its U.S.-based clubs to the U.S. Open Cup in the past. However, the USSF informed the three NASL clubs playing (either directly or through a reserve team) in the NPSL in 2018, that they were not eligible to participate in the tournament, since NPSL teams qualify based on the previous season's results. Neither the New York Cosmos B nor the Jacksonville Armada U-23 were ranked highly enough by the NPSL to qualify, and Miami FC 2 was new to the league. The three clubs appealed this ruling, requesting berths in the tournament. The USSF ultimately reversed its decision and allowed the three teams to participate, bringing the total number of NPSL teams in the tournament to 22.

A play-in round was added to the U.S. Open Cup for the New York Cosmos B, the Jacksonville Armada FC and Miami FC 2. Their opponents were selected from NPSL and Premier Development League (PDL) qualified teams by geographical proximity and a random draw. The three selected teams were given the option to host the matches, which all three elected to do. The New York Cosmos B were drawn against fellow NPSL side the Brooklyn Italians, while the Jacksonville Armada FC and Miami FC 2 drew PDL clubs The Villages SC and FC Miami City, respectively. The Italians defeated the Cosmos,  while the Armada topped The Villages,  and Miami FC 2 beat FC Miami City.

In the first round of the U.S. Open Cup, NPSL clubs had seven wins in 12 matches against PDL teams           and won four of seven matches with local qualifiers. One first-round mach pitted two NPSL teams squaring off against each other.

NPSL clubs lost seven of their nine second-round matches against United Soccer League (USL) opponents. Elm City Express defeated Seacoast United Phantoms in the only second-round match featuring NPSL and PDL teams. One second-round match was an all-NPSL Miami derby with Miami United FC beating Miami FC 2.

In the third round of the U.S. Open Cup, Elm City Express fell to USL side Charleston Battery, and FC Wichita fell to local qualifier NTX Rayados. Miami United FC secured a road win against fellow Florida NPSL side Jacksonville Armada to become the only NPSL team to reach the fourth round of the tournament.

Miami United FC hosted Orlando City SC of Major League Soccer (MLS) in the fourth round of the U.S. Open Cup. Orlando City had 70% of the ball possession and was never really challenged in a 3–0 victory. The Orlando City goalkeeper need to make only one save.

Overall, NPSL clubs had 16 wins and 18 losses against non-NPSL opponents in the U.S. Open Cup. They split their eight matches against local qualifiers, won 10 of 15 matches against PDL teams, lost eight of 10 matches against USL clubs and lost their only match against an MLS squad.

NPSL at the Hank Steinbrecher Cup
The 2017 NPSL champion Elm City Express represented the league at the 2018 Hank Steinbrecher Cup and the title U.S. National Amateur Champions. Matches were played at Veterans Memorial Stadium in New Britain, Connecticut, less than an hour's drive from the Express's home in New Haven.

The Express lost its semifinal match, 2–0, to defending Steinbrecher Cup winner Michigan Bucks of the PDL,

In the third-place match, the Express conceded a goal in second-half stoppage time and fell to the 2017 National Amateur Cup champions Lansdowne Bhoys FC of the Cosmopolitan Soccer League, 2–1.

Regular season
In the Keystone Conference, FC Motown started the season with nine straight wins before dropping a 2–1 decision at home to West Chester United SC in their final match. The loss eventually cost FC Motown home-field advantage in the Northeast Region Final against the New York Cosmos B. Torch FC occupied the bottom of the Keystone Conference, losing all 10 of their matches and scoring only eight goals while conceding 50.

The New York Cosmos B dominated the North Atlantic Conference, winning all 10 of their matches and conceding only eight goals while scoring 40. After starting the season 2–3–2, defending NPSL champion Elm City Express won its final three matches, culminating with a 6–4 road win over Rhode Island Reds F.C. in a winner-take-all showdown for the final North Atlantic Conference playoff berth. In five home matches, the Seacoast United Mariners went pointless, were shut out four times and were outscored, 14–2. The Mariners suffered shutout losses in three of their five road matches but managed draws in the other two.

FC Baltimore and Northern Virginia United FC entered their final regular-season matches with identical 6–2–1 records. FC Baltimore took the top seed in the Mid-Atlantic Conference with an 8–2 home victory over Charlottesville Alliance FC, while Northern Virginia United lost on the road to Virginia Beach City FC, 7–1. A road draw against Charlottesville Alliance in its final regular-season match was just enough for FC Frederick to win a standings tiebreaker over Virginia Beach City and claim the final Mid-Atlantic playoff berth.

The Laredo Heat finished with the best overall regular-season record in the NPSL and was the only team in the South Region with a perfect record, outscoring its opponents, 37–4. The Heat conceded only one goal in five home matches while scoring 20. The Shreveport Rafters FC claimed the second playoff berth in the Blue Group of the Lone Star Conference, when Katy 1895 FC suffered a 9–0 home loss to the Houston Dutch Lions FC in their final regular-season match. Tyler FC lost all 10 of their matches, scoring just seven goals while conceding 54. In their opening match of the season hosting the Shreveport Rafters, Tyler scored a late second-half goal to cut their deficit to 2–1 but could not get the equalizer. They were never within a goal of the winning score for the rest of the season, and they were shut out five times.

The top three clubs in the Sunshine Conference made the conference the most competitive in the league. Eventual NPSL champions Miami FC 2, who topped the Sunshine Conference table, had a loss and three draws in its four regular-season matches against second- and third-place finishers Jacksonville Armada and Miami United. However, Miami FC 2 won all eight of their matches against their other four conference opponents. Both matches between the Armada and Miami United ended in draws. At the bottom of the conference, Storm FC scored only one goal all season. It came at home against Naples United FC in a 1–1 draw, the only match Storm did not lose. Storm was outscored 27–1 at home and 14–0 on the road.

After starting the season 2–3–0, the Little Rock Rangers closed by winning their final five matches. However, it was not enough to catch FC Wichita in the Heartland Conference. Wichita started the season 7–0–0 before stumbling to the finish line with two losses (including one to the Rangers) and a draw in their final three matches. Ozark FC lost all five of their home matches and were outscored, 9–2. Ozark was outscored, 13–2, on the road but did manage a draw against Saint Louis Club Atletico.

Chattanooga FC went 4–0–3 in the first half of the season and 4–2–1 in the second half to take the top seed in the Southeast Conference. The Atlanta Silverbacks were 4–4–2 in their first 10 matches and 3–0–1 in their final four to take second place. Chattanooga and the Silverbacks met in the final match of the regular season and played to a 1–1 draw at Atlanta Silverbacks Park, but Chattanooga entered the match with a four-point lead in the standings.

Minneapolis City SC was the only undefeated team in the West Region, posting a record of 10–0–4 to win the North Conference title. They were 6–0–1 at home. LaCrosse Aris FC went winless at 0–13–1. Oddly, LaCrosse Aris earned their only point of the season with a scoreless draw at home against conference champion Minneapolis City.

AFC Ann Arbor won the Great Lakes Conference title and claimed the second seed in the Midwest Region playoffs with a 9–1–2 record, losing only on the road to second-place Grand Rapids FC. FC Columbus won both of its matches against Grand Rapids. Grand Rapids started the season 5–1–1 in their first seven games but closed by going 2–2–1 in their final five, including the pair of losses to Columbus. Meanwhile, Columbus followed a 1–2–2 start by going 5–1–0 over the next six games to put themselves in position to take the conference's second playoff berth. With Grand Rapids having completed their schedule with a 7–3–2 record, Columbus was 6–3–2 and holding the tiebreaker over Grand Rapids heading into their final match at the 2–5–4 Milwaukee Torrent. The Torrent got the better of Columbus, 1–0, with a goal in the 87th minute and denied them a trip to the postseason. The late-season stumble by Grand Rapids cost them home-field advantage in their Midwest Region Quarterfinal match against Duluth FC. At the bottom of the Great Lakes Conference, FC Indiana lost all 12 of their matches, scoring only four goals while conceding 75. Indiana was outscored on the road, 42–0, in six matches. In Indiana's only match decided by a single goal, the Torrent scored in the 78th minute to break a 2–2 tie and held on for the win.

With the East Conference title on the line, the Erie Commodores FC hosted Cleveland SC in the final match of the regular season for both clubs, who each had identical 7–1–3 records. Cleveland held the standings tiebreaker and needed only a draw for the conference championship, because it had won the first match between the teams, 3–2. Cleveland's 70th minute goal was not enough to overcome two first-half tallies by the Commodores who held on for the win. With Ann Arbor likely to win as they finished up their regular season at home against pointless Indiana, the Commodores and Cleveland were nearly assured at game time that they would be playing each other in the West Region Quarterfinals, and the East Conference champions would host. After starting the season 3–3–3, the Rochester Lancers won their final three matches, but it was not enough to challenge the Commodores and Cleveland for a playoff berth. The Greater Bighamton FC Thunder lost all 12 of its matches, scoring nine goals and conceding 66.

FC Golden State hosted ASC San Diego in a showdown for the Southwest Conference title in the final match of the regular season for both clubs. Golden State entered the match in first place by one point with an 8–1–2 record, their only loss coming at San Diego. ASC San Diego was in second place at 8–2–1, having lost both their matches against Orange County FC. After Golden State built a 2–0 lead, ASC San Diego struck in the 71st, 76th and 79th minutes to win the match, 3–2, and claimed the Southwest Conference championship. The first and third goals in ASC San Diego's dramatic comeback were tallied by their leading goalscorer, Amani Walker. Two days later, Orange County, at 7–1–3, had a chance to claim second place in the Southwest Conference and avoid the plain-in game, if they could earn a road win against Riverside Coras USA. The second-place team in the Southwest Conference would also have home-field advantage in the West Region Quarterfinals. Orange County's Peter Gregory scored his second goal of the match in the 76th minute to break a 2–2 deadlock that had stood since halftime. However, Coras tied the match five minutes later on an own goal, the second Orange County had conceded in the match, and the game ended in a draw.

El Farolito went undefeated at 9–0–5 to win the Golden Gate Conference championship. After starting the season 0–3–2, the Sonoma County Sol finished 7–1–1 to claim the final Golden Gate Conference playoff berth. The Sol and the East Bay FC Stompers entered their June 9 match with identical 3–4–3 records. A go-ahead goal in the 68th minute by NPSL leading goalscorer Omar Nuño was the difference in a 3–2 home win for the Sol. Following the win over the Stompers, the Sol outscored its opponents, 16–0, in its final three matches. FC Davis started the season 3–1–5 but lost their final five matches to fall out of the playoff picture.

Spokane SC Shadow and FC Mulhouse Portland were the only two teams in the Northwest Conference with winning records and claimed the conference's two playoff berths. The Shadow went undefeated at 7–0–5 to claim the conference championship. In head-to-head matchups of the conference leaders, the Shadow had a win and a draw in its two home matches with Portland, which were played on consecutive days, and the only match played in Portland ended in a tie.

Playoffs
With some conferences still playing regular-season matches, the NPSL postseason got underway on June 30, with the Southwest Conference Play-in Game. An early goal by Jonathan Bryant put Orange County in the lead, but a red card issued to Michael Bryant in the 31st minute forced them to play down a man. Daniel Crisostomo doubled Orange County's lead in the 70th minute. A dangerous challenge and a scuffle in the 82nd minute resulted in two red cards for Arizona and a yellow card for Orange County. Cody Shelton scored in the 90th minute to seal Orange County's 3–0 victory. Bennett Sneddon kept the clean sheet.

The Lone Star Conference Quarterfinals were played on July 7. The sixth-seeded Shreveport Rafters FC pushed the Houston Dutch Lions FC to extra time with the match scoreless. Jacob Powell got the Dutch Lions on the board in the third minute of extra time. Ángel Lopez followed with a goal in the final minute before the first half of extra time expired. Dylan Armstrong rounded out the scoring in the 115th minute to give the Dutch Lions a 3–0 victory. Sullivan Lauderdale earned the 120-minute shutout.

The Fort Worth Vaqueros FC dominated FC Brownsville, 5–0, in the other Lone Star Conference Quarterfinal. Jamie Lovegrove and Kallé Soné each contributed a brace, and Jesse Miralrio scored the other goal. Grant Makela kept a clean sheet for the Vaqueros.

The West Region Quarterfinals were played on July 7 and 8. El Farolito got a first-half goal from Arnhold Rivas to take the lead over the Sonoma County Sol but had to play with 10 men after Ademar Rodríguez drew a red card in the 62nd minute. The Sol could not get the equalizer, and Camilo Campo provided another goal in the 90th minute to give El Farolito a 2–0 win. Francisco Rene Garcia recorded the shutout.

For the third time in three matches this season, Orange County FC defeated ASC San Diego. San Diego's leading scorer Amani Walker put them on the board first in the 51st minute. However, Jose Montes de Oca and Daniel Crisostomo both scored in the 58th minute to turn the match around. Dakota Collins provided insurance for Orange County in the 84th minute, and Orange County secured a 3–1 victory over the Southwest Conference champions.

The Northwest Conference champions Spokane SC Shadow got a goal from Micheal Ramos in the 7th minute of their West Region Quarterfinal to take an early lead. However, Christian Thyron replied a minute later for FC Mulhouse Portland. Fred Braun gave Portland a 2–1 lead in the 40th minute, and the Shadow was unable to equalize, suffering its first loss of the season.

FC Golden State got goals from Gabriel Henrique Silva, Allisson, Gustavo Villalobos and Jose Perez-Flores and cruised to a 4–2 West Region Quarterfinal vitory over CD Aguiluchos USA. Simon Rawnsley and Anthony De Souza scored goals for Aguiluchos.

The Southeast Conference Quarterfinals were played on July 10. Both lower seeds who had losing records during the regular season prevailed with road wins. The Georgia Revolution FC upset the New Orleans Jesters, 3–2, on goals by Ehjayson Henry, Isaac Promise and Jumar Oakley. Oliver Roberts scored both goals for the Jesters.

Asheville City SC got goals from Siavash Jamehdar, Elma Nfor and Tyson Hichman to win the other Southwest Conference Quarterfinal over Inter Nashville FC. Jonathan Remond scored in the 90th minute to spoil the shutout.

Nine NPSL playoff matches were played on July 11. Led by two goals from Christopher Katona, FC Motown beat FC Monmouth, 4–1, in the Keystone Conference Semifinals. Walter Calderon and Christopher Riordan also scored for Motown. Chase Covello scored Monmouth's goal.

In the other Keystone Conference Semifinal, Junior Lone Star FC fell behind West Chester United SC, 2–1, when they conceded an own goal in the 41st minute. Three minutes into the second half, Junior Lone Star tied the match on Anthony Allison's second goal of the game. Extra time did not settle the matter, and West Chester United advanced on penalty kicks, 4–3. Charles Wilson's goal in the 12th minute had given United an early 1–0 lead.

The New York Cosmos B and defending NPSL champion Elm City Express each held one-goal leads in the first half of their North Atlantic Conference Semifinal match. Bljedi Bardic scored both Cosmos B goals, and Tyler Carlos had both tallies for the Express. Neither team scored in the second half. The Cosmos B broke through in extra time on goals by Wojciech Wojcik in the 111th minute and Zaire Bartley in the 112th minute. Since the Cosmos B had the best regular-season record in the Northeast Region, the berth in the North Atlantic Conference Final guaranteed them a spot in the region semifinals.

James Thristino's hat trick led the Brooklyn Italians to a 3–0 victory over Hartford City FC in the other North Atlantic Conference Semifinal. Michael Bernardi kept a clean sheet for the Italians.

J. C. Banks and Ciarán Kilduff each had a brace to lead the Jacksonville Armada FC to a 4–1 win over Miami United FC in the Sunshine Conference Semifinal. Nicolas Micoli scored for United.

After Arthur Rogers scored in the 41st minute to give the Houston Dutch Lions FC a lead in the Lone Star Conference Semifinals, the Midland-Odessa Sockers FC temporarily rescued their season, when Maxiliano Galizzi scored in the second minute of second-half stoppage time. Yinka Lawal broke through for the Dutch Lions, scoring in the 113th minute. Jacob Powell added an insurance goal in the second minute of extra-time stoppage time. Two minutes later, Andres Felipe Rodriguez-Becerra scored from the penalty spot for the Sockers, but the referee blew the final whistle shortly thereafter.

The Laredo Heat got a brace from Gabriel Rodriguez, and Rafael Montabes added a goal to lead the Heat to a 3–1 Lone Star Conference Semifinal win over the Fort Worth Vaqueros FC. Declan O'Shea scored for the Vaqueros in the 59th minute to spoil the shutout.

The Little Rock Rangers and Tulsa Athletic were engaged in a scoreless duel in the Heartland Conference Semifinals until Donald Benamna scored in the 90th minute to give the Rangers a 1–0 victory. Walid Birrou kept a clean sheet for the Rangers.

Matt Clare's brace led FC Wichita to a 4–0 Heartland Conference Semifinal win over Saint Louis Club Atletico. Leonardo Perez and late substitute Teylor Cubero also scored for Wichita in a game free from disciplinary actions. Mark Weir recorded the shutout.

Three NPSL playoff matches were contested on July 12. Saidou Toure scored in the 60th minute to give FC Frederick, who qualified for the postsesaon by winning a standings tiebreaker, a lead over Northern Virginia United FC in the Mid-Atlantic Conference Semifinal. Collin Verfurth responded with the equalizer three minutes later, but that was all the scoring for regulation time. United went in front in the 97th minute on a goal by Christopher Welsh, but Brian Flatter responded for Frederick three minutes later, and the match went to penalty kicks. Bilal Hassane put home the winner on Frederick's fifth kick, giving them a 4–3 edge.

The Georgia Revolution FC held top seed Chattanooga FC scoreless in their Southeast Conference Semifinal match, until Juan Hernandez-Mendizabal curled a free kick around the Revolution's wall to give Chattanooga a 1–0 lead in the 73rd minute. Joao Costa added an insurance goal in the 89th minute, and Philip D'Amico kept a clean sheet in Chattanooga's 2–0 victory.

Asheville City SC kept the Atlanta Silverbacks FC off the scoreboard in the other Southeast Conference Semifinal, until Aaron Walker scored in the 68th minute, and Nyambi Jabang followed two mintes later. Bryce Billington recorded the shutout in a 2–0 win.

The Midwest Region Quarterfinals were played on July 13 and 14. The Erie Commodores FC hosted Cleveland SC at McConnell Family Stadium for the second time in six days. The Commodores had won the previous match and claimed the East Conference title and home-field advantage in this clash. After Vincent Bell scored the second of his three goals in the 56th minute to give Cleveland a 2–0 lead, Jacob Alatorre received a par of yellow cards a minute later to put the Commodores down a man. Antonio Manfut's goal in the 63rd minute put Cleveland up, 3–0, and Bell struck again in the 76th minute to complete the scoring in a 4–0 Cleveland victory. Austin Solomon got his second yellow card in the 89th minute, and the Commodores finished the match playing with only nine men. Marijo Musa kept a clean sheet.

Duluth FC went ahead of Grand Rapids FC in the other Midwest Region Quarterfinal, 2–0, on goals from Ryan Tyrer in the 46th minute and David Rice in the 51st minute. However, Grand Rapids mounted a furious comeback, getting goals from Matthew Whelan in the 83rd minute and Kenroy Howell in the second minute of stoppage time to tie the score. After a scoreless 30 minutes of extra time, the teams went to penalty kicks. Trent Vegter and Joe Broekhuizen missed Grand Rapids's third and fourth kicks, respectively. Captain Kyle Farrar's goal on Duluth's fifth penalty shot made it 4–3 and sent Duluth to the region semifinals.

All seven conferences that have conference championship matches staged them on July 14. After Joshua Fawole put FC Baltimore in the lead in the 18th minute, FC Frederick responded with goals by Justin Lee in the 26th minute and Graham Guidry in the 47th minute to earn an upset victory. Frederick, who qualified for the playoffs on the regular season's final day by a standings tiebreaker and had to overcome a one-goal deficit in extra time and win a penalty-kick shootout in the conference semifinal had overcome the odds to beat Baltimore, to whom they lost both regular-season matches, and win the Mid-Atlantic Conference title. The loss by Baltimore meant they needed both New York Cosmos B and FC Motown to win their conference titles in order to reach the Northeast Region Semifinals as the wildcard.

West Chester United SC, who had been responsible for FC Motown's only regular-season loss, took an early lead over Motown in the Keystone Conference Final on Charles Wilson's goal in the 28th minute. The score remained 1–0, until Lucas Terci equalized for Motown in the 90th minute. No goals were scored in extra time, and the match went to penalty kicks. Down, 4–3, in the shootout and needing a goal on their fifth kick, United goalkeeper Charlie Sales failed to score and gave Motown the Keystone Conference championship and a trip to the region semifinals. The loss eliminated West Chester United, who had 2.1 average points per game, since FC Baltimore, who averaged 2.2 had already lost the Mid-Atlantic Conference Final.

James Thristino's goal in the 67th minute gave the Brooklyn Italians a lead over the New York Cosmos B. Zaire Bartley scored an equalizer for the Cosmos B in the 75th minute. However, two minutes later, Rafael Garcia was issued a red card for violent conduct, and the Cosmos B were forced to play with 10 men. Neither team was able to score in the balance of the second half or extra time, and the match went to penalty kicks. After Thomas Suchecki missed the Italians' fourth kick, Jonathan Borrajo scored to give the Cosmos B a 5–3 win in the shootout and the North Atlantic Conference title. The Italians and FC Baltimore had identical 7–2–1 regular-season records. Baltimore won the tiebreaker for the Northeast Region wildcard on average goal difference per game at 2.7 compared with 2.2.

Kris Tyrpak's goal in the eighth minute staked Miami FC 2 to a 1–0 lead over the Jacksonville Armada FC in the Sunshine Conference Final. The Armada tied the match in the 29th minute on Ciarán Kilduff's goal. Five minutes later, Darío Suárez gave Miami FC 2 another lead. Tyrpak scored again in the 53rd minute, and Miami FC 2 went on to a 3–1 victory and the Sunshine Conference championship in a game free from disciplinary actions by the referee.

Philip D'Amico of Chattanooga FC and Bryce Billington of the Atlanta Silverbacks FC both kept clean sheets for 120 minutes, and the Southeast Conference Final was decided by penalty kicks. On the Silverbacks's third and fourth penalty kicks, D'Amico made saves but was called for moving before the ball was kicked. The Silverbacks scored on both re-kicks. With the shootout tied at 5, Cameron Woodfin missed Chattanooga's sixth kick. Brian Pretel followed with a goal to win the shootout for the Silverbacks, 6–5, and give Atlanta the Southeast Conference title.

FC Wichita and the Little Rock Rangers also played 120 scoreless minutes in the Heartland Conference Final. Mark Weir recorded the shutout for Wichita, and Walid Birrou kept the clean sheet for the Rangers. Andres Ochoa failed to score on Wichita's third kick, and Donald Benamna scored to make it 5-for-5 for the Rangers and give them a 5–3 win in the shootout and the Heartland Conference title.

Arthur Rogers scored two first-half goals, the second on a penalty kick to put the Houston Dutch Lions FC in front of the Laredo Heat in the Lone Star Conference Final. The Heat battled back on goals by Ziyad Fares in the 67th minute and Petteri Pietola in the 74th minute to send the match to extra time. Tor Trosten scored twice in extra time, in the 96th and 101st minutes, to give the Heat the lead. Yinka Lawal answered for the Dutch Lions in the 104th minute, but Houston could not get an equalizer, and the Heat won the Lone Star Conference championship.

Home teams were able to win only four of the seven conference championship matches. Four of the seven conference championship matches were decided by penalty kicks, and one more was decided in extra time. Three teams that were trailing in conference championship matches scored equalizers in the 74th minute or later and ended up winning their matches.

The West Region Semifinals were contested on July 14 and 15. El Farolito fell behind FC Mulhouse Portland on a Reed McKenna goals in the 21st minute. Luis Galeano added an insurance goal in the 77th minute, and Portland went on to a 2–0 road victory. Scott Dalrymple kept the clean sheet.

Tomas A. Canale's brace led Orange County FC to a 4–2 road win over FC Golden State in a West Region Semifinal match. Golden State got on the board first when Gabriel Henrique Silva scored in the 22nd minute, but Canale's goals in the 33rd and 63rd minutes sandwiched a Dakota Collins tally in the 61st minute. Adrien Perez scored in the 84th minute to cut Golden State's deficit to 3–2, but Kevin Jeon's 90th minute goal sealed the victory for Orange County.

The South Region Semifinals were played on July 17. Miami FC 2 and the Atlanta Silverbacks FC exchanged first-half goals. Sean McFarlane Jr. opened the scoring for Miami in the 22nd minute, and Thierry Jules answered in the 36th minute. Atlanta's David Koloko drew a red card for serious foul play in the 79th minute, and Miami capitalized on the man advantage two minutes later, when Kris Tyrpak scored the winner in a 2–1 victory.

The Little Rock Rangers took an early lead over the Laredo Heat in the other South Region Semifinal, when Trevor Reed scored in the 31st minute. The Heat got the equalizer from Rodave Murray in the 87th minute to send the game to extra time. Donald Benamna's goal in the 115th minute gave the Rangers a 2–1 upset victory and handed the Heat its first loss of the season.

The Northeast Region Semifinals were contested on July 18. The New York Cosmos B got a brace from Zaire Bartley and a clean sheet from Kevin Tenjo to beat FC Frederick, 2–0.

A brace by Daryl Kavanagh and a goal by Christopher Katona led FC Motown to a 3–0 victory over FC Baltimore in the other Northeast Region Semifinal. Abdou Karim Danso earned the shutout.

The final four teams in the Midwest Region met in Ann Arbor, Michigan on July 20, for the region semifinals. Duluth FC took an early lead over the region's top seed, Minneapolis City SC, on a 17th minute goal by their captain, Kyle Farrar. Branden McGarrity responded for Minneapolis City in the 36th minute, and the score remained tied, until Ricardo Ramos converted a penalty kick in the 115th minute, giving Duluth a 2–1 victory.

Serge Gamwanya scored a goal in the 55th minute, and AFC Ann Arbor made it hold up in a 1–0 Midwest Region Quarterfinal victory over Cleveland SC. Nick Barry kept the clean sheet for Ann Arbor.

All four region final matches were contested on July 21. Miami FC 2 cruised to a 3–0 victory over the Little Rock Rangers to win the South Region championship. Jaime Chavez, Dylan Mares and Darío Suárez each scored for Miami FC 2, and Mario Daniel Vega earned the shutout.

Walter Calderon, Christopher Katona and Dilly Duka each had a goal to give FC Motown a 3–0 lead over the New York Cosmos B. Ivan Berterame scored two goals for the Cosmos B during second-half stoppage time, but it was too little, too late, and Motown held on for a 3–2 win and the Northeast Region championship.

Ryan Tyrer opened the scoring for Duluth FC in the 12th minute of the Midwest Region Final against AFC Ann Arbor. Chrispinus Odhiambo answered in the 23rd minute, but Ann Arbor conceded and own goal a minute later to fall behind again. Duluth increased their lead to 3–1, when their captain, Kyle Farrar, scored in the 39th minute. Jack Cawley's 42nd minute goal brought Ann Arbor within a goal at the half. Azaad Liadi kept Ann Arbor's hopes alive with a goal in the forth minute of second-half stoppage time. Duluth substituted Alberto Ciroi for NPSL Golden Glove winner Jan Hoffelner in the 118th minute in preparation for a penalty kick shootout. In the second minute of extra-time stoppage time, Ciroi took a kick to the head from Odhiambo, who was issued a yellow card. Three other players drew yellow cards in the ensuing scuffle. Neither team scored in extra time. In the shootout, Ciroi saved Matthieu Braem's attempt on Ann Arbor's second kick and Michael Shaikly's effort on their fourth kick. Ann Arbor goalkeeper Nick Barry extended the shootout by saving Aidan Hill's attempt on Duluth's fourth kick. Kyle Breitmeyer's shot hit the crossbar and then Ciroi's back before settling into the net and keeping Ann Arbor in the match. Liam Moore won the shootout for Duluth, 4–3, when he scored on their fifth kick, and Duluth celebrated the Midwest Region championship.

Orange County FC and FC Mulhouse Portland played a wild first half in the West Region Final. Both teams held the lead for stretches of a half that ended 3–3. Orange County got goals from Tomas A. Canale, Michael Bryant and Dakota Collins. Fred Braun, Christian Thyron and Alex White scored for Portland. Orange County took a 4–3 lead, when Cody Shelton scored in the 53rd minute, but Portland responded in the 60th minute with Braun's second goal of the match. Reed McKenna's goal put Portland in front in the 78th minute. Jonathan Bryan drew a red card for a serious foul play in the 84th minute that forced Orange County to play with 10 men. Luis Galeano's 90th minute goal put away a 6–4 win for Portland that gave them the West Region championship.

The NPSL National Semifinals were played on July 28. Miami FC 2 got goals from Ariel Martínez (on a penalty kick), Sean McFarlane Jr. and Jeff Michaud to beat the Duluth FC, 3–0. Mario Daniel Vega kept the clean sheet for Miami.

In the other semifinal match, Dilly Duka put FC Motown in front of FC Mulhouse Portland with a goal in the 55th minute. Nick Evans responded for Portland in the 63rd minute to tie the score. David Nigro, who had just entered the match as a substitute in anticipation of a penalty-kick shootout, scored the winner in the first minute of extra-time stoppage time to send Motown to the NPSL Final.

FC Motown hosted Miami FC 2 in the NPSL Final on August 4. Miami struck first on a Jonny Steele goal in the 33rd minute. Dilly Duka answered for Motown two minutes later. Motown was reduced to playing with 10 men in the 58th minute, when Christopher Riordan drew his second yellow card. One minute later, Dylan Mares's goal put Miami back into the lead. Jeff Michaud added an insurance goal in the 81st minute, and Miami FC 2 went on the win the NPSL championship in its inaugural season.