The 2006 Big Ten Conference baseball tournament was held at Ray Fisher Stadium on the campus of the University of Michigan in Ann Arbor, Michigan, from May 15 through 19.
The top six teams from the regular season participated in the double-elimination tournament, the twenty fifth annual tournament sponsored by the Big Ten Conference to determine the league champion.
Michigan won their seventh tournament championship and earned the Big Ten Conference's automatic bid to the 2006 NCAA Division I baseball tournament.
As in the previous four years, the top two seeds received a single bye, with the four lower seeds playing opening round games.
Teams that lost in the opening round played an elimination game.