The 2006 Southern Conference Baseball Tournament was held at Joseph P. Riley, Jr. Park in Charleston, SC from May 23 through May 27. Second seeded College of Charleston 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.