The 2006 America East Conference baseball tournament took place from May 25 through 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.
The top four finishers from the regular season were seeded one through four based on conference winning percentage only. They then played in a double-elimination format. In the first round, the one and four seeds were matched up in one game, while the two and three seeds were matched up in the other.
The following players were named to the All-Tournament Team.
Maine outfielder Mark Ostrander was named Most Outstanding Player.