Flynn began his professional career in his native Northern Ireland with Ballymena United, after being spotted by Belfast-based scout Dominic McEnhill playing in the Down and Connor League for Newhill U16s. He was then spotted by Blackburn Rovers club scout Barry Hunter in late 2007, signing for the Lancashire club in January 2008.
Blackburn Rovers
The defender spent 2 years at Blackburn and during this time failed to make a competitive appearance for the club. Flynn had two loan spells at Chester City and Accrington Stanley in the 2009–2010 season.
Ross County
Flynn signed for Ross County in the summer of 2010 but only managed to make 23 appearances in his two seasons at Victoria Park, scoring 4 goals., including one that secured County'sFirst Division status in the 2010–2011 Season against Falkirk, who he would eventually sign for in the summer of 2012.
Falkirk
Flynn signed for Falkirk from Ross County in the summer of 2012 for a nominal fee. He made his debut for the club in the Ramsden's Cup against Stirling Albion on 28 July 2012. Flynn was a first-team regular in his first season at Falkirk, and after a nervy first few games, developed a solid defensive partnership with the vastly experienced club captainDarren Dods. In his second season, with the arrival of Will Vaulks and David McCracken, he found himself more frequently as back-up on the bench. Flynn did however start all four of Falkirk's Scottish Premiership Play-Off games; he was heavily praised for his performances in these matches, in particular the Quarter Final Second Leg 3-1 victory after extra time against Queen of the South on 10 May 2014. Fans were widely impressed and grateful for Flynn's professionalism in the play-off matches, having been on the bench for most of the season and having already agreed a deal to sign for Cliftonville for the following season. Flynn's last appearance in a Falkirk shirt was to be in the Play-Off Semi-Final Second Leg defeat to Hamilton Academical on 18 May 2014.
Cliftonville
Flynn signed a pre-contract with Cliftonville in March 2014 and will join them for the 2014–15 season. Flynn was also to set up his own football coaching business 'JF Football Fitness' on his return to Northern Ireland.