Flynn made his National Football League debut for Dublin against Westmeath and scored a goal in the process, helping guide his team to a first-round victory.

On 18 September 2011, Flynn helped Dublin claim their first All-Ireland title in sixteen years, as they beat Kerry at Croke Park.

On 22 September 2013, Dublin won the All-Ireland Senior Football Championship with a big help from Paul Flynn in the half-forward line wearing number 10.

In 2012 after reaching the All Ireland Semi-Final and losing to Mayo, he was selected as Dublin's lone All Star alongside roommate and friend Michael Murphy.

Flynn's achievement, both in terms of overall awards won and in earning the distinction of becoming the first to win four in a row in almost 30 years, ranks high up in the overall All Stars hall of fame.