Flynn made his Dublin debut when appearing as a second-half substitute in Dublin's first-round O'Byrne Cup victory over Wicklow on 5 January 2008 in Parnell Park. 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. He made his Championship debut against
Westmeath on 29 June 2008. On 18 September 2011, Flynn helped Dublin claim their first All-Ireland title in sixteen years, as they beat
Kerry at Croke Park. He was awarded his first
All Star Award for his performances for Dublin in the half forwards in 2011. Under Pat Gilroy's management term Paul Flynn became a regular in the Dublin half-forward line and was selected as Dublin's lone All Star in 2012. In 2013, he complained about a lack of intensity of the Dubs and he brought amazing fitness levels and intensity to the team. 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. He played twice for
Ireland against
Australia in the
2013 International Rules Series. In 2016 Flynn helped his club Fingallians to win the Dublin Intermediate Club Championship. That same year they went on to reach the semi-final of the Leinster Intermediate Club Championship which included a victory over St Josephs of Louth in the process before losing to Rosemount of Westmeath in that semi-final. In May 2019, it was confirmed that Flynn had stepped away from the Dublin senior football team.{{cite web|url=https://www.independent.ie/sport/gaelic-games/gaelic-football/ive-loved-every-minute-of-my-journey-fourtime-all-star-paul-flynn-calls-time-on-his-dublin-career-due-to-back-injury-38067844.html ==All Stars==