Flynn was drafted by the Green Bay Packers in the seventh round (209th selection overall) of the 2008 NFL Draft. On July 23, he was signed to a four-year rookie contract through the 2011 season. In 2008, Flynn won the competition for the back-up role to Aaron Rodgers, beating out fellow rookie and second-round pick Brian Brohm. Flynn was seen as being less talented than Brohm because of Brohm's superior size, arm and foot speed, coupled with the fact that Brohm was selected much higher in the draft compared to Flynn.