The 2006 NCAA Division II men's basketball tournament involved 64 schools playing in a single-elimination tournament to determine the national champion of men's NCAA Division II college basketball as the culmination of the 2004–05 NCAA Division II men's basketball season.

It was won by Winona State University and WSU's John Smith was the Most Outstanding Player.

[1] Location: Walter Sillers Coliseum Host: Delta State University Location: Royal Brougham Pavilion Host: Seattle Pacific University Location: Richard F. Scharf Alumni Fieldhouse Host: St. Joseph's College Location: Barco-Stevens Hall Host: Virginia Union University Location: McCown Gymnasium Host: Winona State University Location: Wilson Gym Host: Barton College Location: Merkert Gymnasium Host: Stonehill College Location: Meyer Wellness & Sports Center Host: Southwest Baptist University Location: MassMutual Center Hosts: American International College and Naismith Memorial Basketball Hall of Fame