Flynn was drafted by the Green Bay Packers in the 7th round (209th overall) of the 2008 NFL Draft. On July 23, he was signed to a four-year contract through the 2011 season. He is now Green Bay's second-string quarterback. He won the back-up role to Aaron Rodgers by beating out fellow rookie and second-round pick Brian Brohm. The battle for the second-string position became the most interesting battle in camp. Flynn was seen as being less talented than Brohm because of Brohm's larger size, and better arm and foot speed.