In the quarterfinals of the 2009 Big East Tournament on March 12 and 13, Flynn led the Orange to a 127–117 win in six overtimes over the favored University of Connecticut Huskies. Flynn played 67 out of a possible 70 minutes on the floor that evening, leading the Orange by scoring 34 points, adding 11 assists and making all 16 of his free throw attempts. The next day, Flynn then played all 45 minutes of Syracuse's 74–69 overtime victory over the West Virginia Mountaineers in the Big East semifinals. He scored 15 points and had 9 assists. Syracuse, however, would eventually fall to Louisville in the Big East championship game, 76–66. For his efforts, Flynn was named the 2009 Big East Tournament's MVP, the fourth player from the losing team to win the award in the tournament's history.