Mike Flynn joined Norwich from Oldham Athletic in 1988 after 40 league games for the Latics. He was unable to break into the City first team and was transferred to Preston North End for a then record £125,000 for whom he made 136 league appearances, scoring 7 goals. He joined Stockport County for £150,000 and captained them in their successful 1996/97 season which saw them gain promotion to Division One and reach the semifinals of the Coca Cola Cup and quarterfinals of the FA Cup. His manager was Gary Megson whilst he partnered Colin Woodthorpe in defence.

Mike was the subject of a £800,000 bid from Birmingham City in February 1999 but this was rejected by the Stockport board. Stockport have offered Mike an improved contract to keep their influential skipper at Edgeley park but he stated that he is "hoping that Birmingham will come back with a higher offer" as Birmingham offered a better chance of reaching the Premiership. Mike handed in a transfer request in March 1999 but has since signed a new contract.

Mike had made 361 league appearances for Stockport by the end of 2000/01 scoring 14 goals. Mike joined Stoke on a two month loan in January 2002 as he did not fit into new Stockport manager Carlton Palmer's first team plans. On 14th March 2002, Stockport cancelled Flynn's contract and he immediately signed for Barnsley.

Mike moved to Blackpool on a three month loan on January 10th 2003. This became a permanent move on March 21st 2003, with Blackpool freeing up wages by loaning Paul Dalglish to Scunthorpe on the same day.

At the end of September 2004, Mike moved to Conference side Accrington Stanley, signing a contract until the end of June 2006. Teammates at Stanley will include Paul Cook and Ged Brannon

In November 2005, Mike was told that he was no longer part of Accrington's first team plans and was free to leave the club. The following week, he joined Hyde United on loan. This became a full transfer in January 2006. He was loaned in November 2006 to Mossley managed by Jason Beckford (brother of former Canary Darren)

Mike is now playing with Radcliffe Borough in the Unibond First Division North and working as a classroom assistant at a special needs school in Oldham where his wife works Accordign to the interview given in the Preston versus Norwich match on 11th August 2007, he enjoys his job so much that he turned down a coaching position with Stockport.

He moved to divisional rivals Salford City in January 2009, where he became assistant manager as well as player.

He later coached at Stockport and Rochdale.