2006 Southern Conference baseball tournament

The 2006 Southern Conference baseball tournament was held at Joseph P. Riley Jr. Park in Charleston, South Carolina, from May 23 through 27. Second seeded won the tournament and earned the Southern Conference's automatic bid to the 2006 NCAA Division I baseball tournament. It was the Cougars' first SoCon tournament win.

All ten baseball programs in the conference participated in the tournament, with the seventh through tenth place teams playing a single-elimination opening day prior to an 8-team, double-elimination tournament.

Results
Seeding and pairings