The 1999 Southeastern Conference baseball tournament was held at Hoover Metropolitan Stadium in Hoover, Alabama from May 19 through 23. Alabama defeated Arkansas in the championship game, earning the Southeastern Conference's automatic bid to the 1999 NCAA Division I baseball tournament.

The top four teams (based on conference results) from both the Eastern and Western divisions earned invites to the tournament.^{[citation needed]}

Most valuable player G.W. Keller, Alabama