The 1999 Conference USA baseball tournament was the 1999 postseason baseball championship of the NCAA Division I Conference USA, held at USA Stadium in Millington, Tennessee, from May 12 through 17. defeated in the championship game, earning the conference's automatic bid to the 1999 NCAA Division I baseball tournament.
Two play-in games among the four teams with the worst regular season records decided which two teams would have the final two spots in the eight-team double-elimination bracket.