[2][3] Flynn began his career with his hometown club Oldham Athletic first signing apprentice forms in July 1985 before turning professional in February 1987.
In December 1989 Third Division club Preston North End tabled a bid of £125,000 which Norwich accepted enabling Flynn to return to his native north-west of England.
In his time at Deepdale they sold Tony Ellis, Warren Joyce, Alan Kelly, Martin James, Brian Mooney and Mark Patterson.
[2] Shortly after the loan was extended into a third month, Flynn left to join Steve Parkin's Barnsley of the First Division; Stockport gave him a free transfer and promised him a testimonial match, despite his having been with the club for less than the customary ten years.
He played 45 games for Accrington before leaving for Conference North club Hyde United in November 2005 and then in December 2006 Stalybridge Celtic.
In 2007 Flynn signed for Northern Premier League Division One North club Radcliffe Borough, moving to divisional rivals Salford City in January 2009, where he became assistant manager as well as player.