Flynn signed for Coventry City from non-league Halesowen Town in December 1991 and made his debut in August of the following year as a second-half substitute for David Smith in a 2–1 Premier League victory over Middlesbrough at Highfield Road, eventually going on to record 105 games and 10 goals for the Sky Blues over the next 5 years. In August 1995, after being told by then-Coventry manager Ron Atkinson, that he was no longer required at the club.
Derby County
Flynn dropped a division to Division One to become one of Jim Smith's first signings at Derby County for a fee of £250,000. Flynn's time at Derby proved to be successful as he was part of the side which finished runner-up to Sunderland in the 1995–96 Division One table and earn promotion to the FA Premier Leaguefor the first time. Flynn started the Premier League campaign in the Derby first team, scoring an 80th-minute winner at Blackburn Rovers in Derby's 5th game of the season to earn them their maiden win of a season which saw the Rams eventually finish 12th, but eventually found himself pushed to the fringes of the Derby squad, and joined Stoke City on loan in March 1997 where he made five appearances. After 65 games and 3 goals for Derby.
Later career
Flynn made the switch to his boyhood club West Bromwich Albion for a fee of £260,000 in August 1997. As a West Bromwich Albion fan, one of the highlights of his career was when he captained the team. He played 122 games and scored 8 goals for the Baggies. In July 2000, Flynn moved on a free transfer to Tranmere Rovers and spent two years there playing 82 games and scoring 11 goals in all competitions. Flynn signed for Kidderminster Harriers in August 2002 on a free transfer and made 57 appearances scoring two goals before leaving in the September 2003.
Non League
Flynn played 436 games and scored 34 goals in his years as a pro footballer. He joined Evesham United in 2003, staying until 2004 when he moved to Redditch United. He had moved back to Evesham and then back again to Redditch by 2005 and eventually stayed with Redditch until 2008. As well as running his business he joined Bodmin Town in 2008 where he went on to win a league and cup domestic treble, as well as player of the year, managers player of the year and supporters player of the year. In 2009, he joined Mullion as player/manager but left shortly afterward to team up with former Bodmin manager Alan Carey at Falmouth Town. Carey appointed Flynn as player/assistant manager and he remained with the club until joining Penzance in 2011. He returned to Falmouth as a player in March 2012.
