Flynn began his career with his hometown club Oldham Athletic first signing apprentice forms in July 1985 before turning professional in February 1987. He made an immediate impact with the "Latics" going straight into the first team and earning a reputation as a no nonsense centre half. Playing in the Second Division Flynn was attracting attention from some of the bigger clubs and in December 1988 at the age of 19, and after playing 44 games and scoring one goal he signed for First Division club Norwich City for a fee of £100,000.
Norwich and Preston
Flynn's time at Norwich was for him a frustrating one though for in his twelve months with the club he failed to make a single appearance. 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. His time at Preston was, however, a difficult one for although his performances were generally good the club were struggling with some of their better players being sold to boost the club coffers. In his time at Deepdale they sold Tony Ellis, Warren Joyce, Alan Kelly, Martin James, Brian Mooney and Mark Patterson. It therefore came as no surprise when Flynn himself was sold to Stockport County in March 1993 for a fee of £125,000. In Flynn's three-and-a-half years at Preston he had played 162 games scoring eight goals.
Stockport County
Flynn's move to Edgeley Park started a ten-year spell with the club. He won the supporters' Player of the year award in the 1993–94 season. Flynn helped the club to the Second Division play-off final at Wembley where they lost to north west rivals Burnley. The following season saw Flynn given the captain's armband and in the 1996–97 season captained the side to promotion to the First Division as well as to the semi-final of the League Cup, round four of the FA Cup and the Autoglass Trophy northern final. Flynn was an ever-present that season playing a total of 66 games. Flynn's performances had not gone unnoticed and when an £800,000 bid from Birmingham City was rejected by County in February 1999 Flynn was somewhat unhappy. He did though sort things out with County and later on in the year signed a new contract with the club. During the 2001–02 season County began to struggle and when manager Andy Kilner was sacked, it was thought that Flynn might be in the running for the job. It wasn't to be though as just before Christmas 2001 Carlton Palmer was given the job and Flynn was weeks later loaned out to Stoke City. In Flynn's two months at the Britannia Stadium he played thirteen games. 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. In all Flynn played 460 games for "the Hatters", scoring 19 goals. On 18 July 2014 Stockport held a testimonial for Mike Flynn at their home Edgeley Park the event was attended by over 30 Stockport legends including Kevin Francis, Andy Preece and many others. Flynn donated half the money made on the night back into the club.
Barnsley and Blackpool
In little over a year at Oakwell he played just 21 games before in January 2003 returning to the North West with Blackpool, initially on loan and then permanently in March of the same year. Flynn's committed performances made him a favourite at Bloomfield Road and he played more than 50 games for the club, taking his League career tally to 654 games played and 25 goals scored. In 2004 he started the final as Blackpool won the 2003–04 Football League Trophy.
