Flynn was drafted sixth overall in the 2009 NBA draft by the Minnesota Timberwolves, ahead of future two-time MVP Stephen Curry at the point guard position. Expectations were very high for Flynn as he was seen as the future cornerstone point guard for the Timberwolves by GM David Khan. Flynn's stats were solid for his rookie season: he averaged 13.5 points per game and 4.4 assists per game. He showed flashes of stardom, and had some amazing games in the 2009-2010 season. However he was criticized for not playing up to his draft potential, and many people considered him a bust.