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During the 1949–50 English football season, Gillingham F.C. played in the Southern League Division One. It was the fourth season of the club's third spell in the league.

Gillingham also competed in the FA Cup, reaching the second round.

Background and pre-season
Gillingham had been among the founder members of the Football League Third Division in 1920, which was renamed the Third Division South when a parallel Third Division North was created a year later. In 18 seasons between 1920 and 1938, the team consistently struggled, only finishing in the top half of the league table three times. They finished in the bottom two on five occasions, requiring them to apply each time for re-election to the League. The club's fifth application was unsuccessful; Ipswich Town of the regional Southern League received more votes than Gillingham from the Football League's other member clubs in the ballot following the 1937–38 season and thus secured election to the Third Division South. Gillingham initially took Ipswich's place in the Southern League; when competitive football resumed after the Second World War, Gillingham played in the more localised Kent League for one season before returning to the Southern League in the 1946–47 season and winning the championship twice in three seasons.

Southern League Division One
Gillingham finished in fifth place in the Southern League Division One.

FA Cup
As a Southern League Division One team, Gillingham entered the 1949–50 FA Cup at the fourth qualifying round stage; they reached the second round proper where they lost to Yeovil Town.

Southern League Cup
Gillingham lost to Colchester United in the second round of the 1949–50 Southern League Cup.

Players
Charlie Marks made the most appearances, playing 49 times. Harold Williams was the team's top goalscorer, scoring 18 times in just 20 games.

Aftermath
Following the season, the Football League opted to increase the membership of each of the two Third Divisions from 22 to 24 clubs; Gillingham applied for one of the new places in the Third Division South and received the highest number of votes among the applicants, thereby returning to the Football League after 12 years. Chairman Charles Cox told the press "It has been an uphill struggle to get back. Thank God we've done it. We must never find ourselves in that position again."