The 2006 America East Conference Baseball Tournament took place from May 25-27 at Centennial Field in Burlington, Vermont. The top four regular season finishers of the league's seven teams qualified for the double-elimination tournament. In the championship game, third-seeded Maine defeated first-seeded Stony Brook, 5-3, to win its fourth tournament championship (its first under head coach Steve Trimper). As a result, Maine received the America East's automatic bid to the 2006 NCAA Tournament.