1999 Patriot League baseball tournament

The 1999 Patriot League baseball tournament was held on May 17 and 18, 1999 to determine the champion of the Patriot League for baseball for the 1999 NCAA Division I baseball season. The event matched the top three finishers of the six team league in a double-elimination tournament. Second seeded won their third championship and claimed the Patriot's automatic bid to the 1999 NCAA Division I baseball tournament. Pat Klakow of Navy was named Tournament Most Valuable Player.

Format and seeding
The top three finishers by conference winning percentage from the league's regular season advanced to the tournament. The top seed earned a first round by and the right to host the event. The second and third seeds played an elimination game, with the winner meeting the top seed in a best-of-three series.