Born in Newport, Flynn started his career playing for Newport County in 1999. A move to League of Wales club Barry Town beckoned in 2000. After forty goals in two seasons, including a goal in a 3–1 win over F.C. Porto in the second qualifying round of the Champions League, he moved to Wigan Athletic in the 2002–03 season.
Flynn spent a lot of his time on the substitutes' bench as Wigan won Division Two title. He made seventeen appearances in the league, fourteen of which came from the bench, and scored one goal. The next season did not start any better for Flynn as he started just one game and made seven appearances from the bench before he was loaned to then League One side Blackpool, where he started six times in the league and once in the FA Cup before returning to Wigan.
In the January transfer window of that season, Flynn joined Championship strugglers Gillingham on a free transfer. Despite his instant success, and his three goals in sixteen starts, Gillingham were relegated to League One on the last day of the season.
Although injury affected his 2005–06 season, Flynn scored six goals. He took over as captain for the 2006–07 season and became top scorer with twelve goals.
It was announced on 8 May 2007 that Flynn had been offered a new contract with Gillingham. He chose not to sign, and left the club when his contract expired at the end of June 2007.
On 5 July 2007, Flynn signed a one-year contract with Blackpool, with an option for a further year. On 3 December 2007, Flynn scored his first goal for Blackpool in the club's 1–1 away draw against Scunthorpe United. On 7 May 2008 he was released by Blackpool. On 23 July 2008, he became Stan Ternent's fifth signing at League One side Huddersfield Town. He along with 5 other players made his Town debut in the 1–1 draw against Stockport County at the Galpharm Stadium on 9 August 2008. On 27 August he scored his first goal for Huddersfield in the second round of the League Cup against Sheffield United. Town went on to lose the game 2–1. His first league goals for Town came in the 3–2 win over Northampton Town at the Galpharm Stadium on 20 September 2008.
Following a short spell on the sidelines following a hamstring injury, he joined Darlington on loan on 27 November 2008. He made his debut in the 1–0 defeat to Morecambe at Christie Park on 13 December. He returned to Huddersfield on 29 December.
On 4 August 2009, Flynn joined local rivals Bradford City on a free transfer. He made his debut four days later in the 5–0 defeat by Notts County at Meadow Lane and scored his first goal of the 2011–12 season in a 3–2 loss to Leeds United. On 28 April 2012 it was announced that he would leave Bradford as his contract was ended by mutual consent along with teammates Chris Mitchell and Craig Fagan.
On 25 July 2012 he re-signed for home-town club Newport County. In the 2012–13 season he was part of the Newport team that finished 3rd in the league, reaching the Conference National playoffs. Newport County won the playoff final versus Wrexham at Wembley Stadium 2–0 to return to the Football League after a 25-year absence with promotion to Football League Two.
In May 2015 Flynn's playing contract came to an end and it was not extended by Newport.
In January 2017 whilst first team coach at Newport Flynn registered as a player. He made his fourth debut for Newport in the League Two match on 28 January 2017 versus Hartlepool United as a second-half substitute.
In May 2014, alongside his playing role, Flynn took over from Glyn Jones as director of Newport County's youth academy. Academy scholars Regan Poole, Aaron Collins and Tom Owen-Evans made first team debuts under Flynn's guidance. In May 2015 the Academy organisation was restructured in order to comply to FA guidelines. Following his release at the end of his playing contract Flynn applied for the senior role of Academy Manager but was unsuccessful. Flynn left the Academy following the appointment of Grant Kalahar as Academy Manager in June 2015. On 6 August 2015 Flynn joined Welsh Football League Division Two side Undy Athletic as player-manager. On 8 October 2015 Flynn rejoined Newport County as first team coach under new manager John Sheridan. In January 2016 Warren Feeney was appointed team manager and Flynn was retained as first team coach. In July 2016 Newport County appointed Flynn to a newly created role as Football and Business Development Director. In October 2016 Flynn again rejoined the Newport County coaching staff under newly appointed manager Graham Westley
On 9 March 2017 Flynn was appointed caretaker manager of Newport County for the remainder of the 2016–17 season following the sacking of Graham Westley with Newport 11 points adrift at the bottom of League Two. Wayne Hatswell returned to the club as Assistant Manager to Flynn. Flynn led the team to Football League survival, avoiding relegation with a win in the final match of the season and confirming the second 'great escape' in the club's history. On 9 May 2017 Flynn was appointed permanent team manager on a two-year contract.As of match played 23 September 2017