The 2006 Conference USA baseball tournament was the 2006 postseason college baseball championship of the NCAA Division I Conference USA, held at Reckling Park in Houston, Texas, from May 24–May 28, 2006. Rice won the tournament in its first year as a member of the conference, and received Conference USA's automatic bid to the 2006 NCAA Division I baseball tournament. The tournament consisted of eight teams, with two double-elimination brackets, and a single-game final.