Flynn was a former high school and college teammate of guard/forward Paul Harris, whom he played alongside as members of the Minnesota Timberwolves' summer league team.

Flynn was named to the preseason All Big East team[5] and started the season with a 27-point effort against Richmond on November 18, 2008.

[6] Seven days later, Flynn scored 25 points and hit a 3-pointer with 6.4 seconds left in regulation as Syracuse defeated then-No.

With Syracuse clinging to a 52–48 lead, Flynn drove to the hoop and threw down a monstrous dunk over opposing guard Michael Rosario as he attempted to draw a charge.

[8][9][10][11] 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 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.

[12][13] The next day, Flynn then played all 45 minutes of Syracuse's 74–69 overtime victory over West Virginia in the Big East semifinals.

[15] In his first career NCAA tournament game in 2009, Flynn led all scorers in their first-round matchup against Stephen F. Austin, tallying 16 points and 7 assists.

[16] On April 9, 2009, it was announced by Syracuse University that Flynn would declare himself eligible for the upcoming NBA draft.

[17] Flynn officially decided to forgo his final two years at Syracuse and signed with Creative Artists Agency Sports, run by agent Leon Rose, on April 15.

Expectations were very high for Flynn as he was seen as the future cornerstone point guard for the Timberwolves by GM David Kahn.

[19] On October 28, 2009, Flynn made his professional debut and sparked a rally for the Timberwolves, coming back from 19 points down.

On March 15, 2012, Flynn was traded to the Portland Trail Blazers, along with Hasheem Thabeet and a future second-round pick (Will Barton was later selected), for Marcus Camby.

[30] In his first game in the NBL, and after only a few days of preparation, Flynn was impressive with 12 points, eight rebounds, seven assists, and one block and lifted the struggling Tigers to a dominant 96–66 win over the Adelaide 36ers.