Wrexham He became manager of
Wrexham in 1989, and remained in charge until 2001. During his twelve years in charge Wrexham won the
Welsh Cup three times gaining entry to the
Cup Winners Cup. They achieved notable
FA Cup giant-killing victories over reigning league champions
Arsenal and
Premier League West Ham United. At the time of his departure from Wrexham he was the
league's third longest serving manager behind
Alex Ferguson and
Dario Gradi. Cusack's last game in charge on 18 September 2002 had seen Swansea lose 1–0 away to
Boston United and move to last place in the
Football League for the first time in their history. Flynn's first game on 21 September 2002 was no better for Swansea with them losing 1–0 at home to
Torquay United. He set about trying to rebuild the side giving debuts to 21 players in his first season The
following season started well for Swansea and they made the
FA Cup 5th round but after a loss of form, Flynn was replaced by
Kenny Jackett.
Wales Flynn joined the Welsh national set-up in 2004 as under-21 coach. His management of the Welsh under-21 side has seen some of the best results in its history. Flynn came agonisingly close to taking the Welsh team to the
2009 UEFA under-21 Championships, guiding the side to the top of a group containing
France and
Romania, including a superb away win against the latter. Unfortunately, competition rules stipulated that even group winners had to go through a two-legged play-off round in order to qualify, and Wales were knocked out 5–4 on aggregate against their neighbours,
England. Following the departure of
John Toshack as Wales manager in September 2010, Flynn was appointed as Wales caretaker manager. He took charge of two games, both defeats. On 8 October 2010 Wales were beaten 1–0 in Cardiff by
Bulgaria and on 12 October 2010 they lost 4–1 to
Switzerland at
St. Jakob-Park in
Basel. Flynn vacated his position with Wales Under 21s in May 2012 at the end of his contract. He was credited with an important role in the development of
Gareth Bale,
Aaron Ramsey,
Joe Allen and
Wayne Hennessey.
Doncaster Rovers Having already been working for
Doncaster Rovers as a scout, he was appointed as caretaker manager of the club on 7 January following
Dean Saunders move to
Wolverhampton Wanderers. At that point he was assisted by player
Rob Jones who had been briefly installed as caretaker earlier that morning. On 17 January Flynn was confirmed as permanent manager with a contract till the end of the season. His first game in permanent charge of Doncaster on 19 January 2013 saw his side win 2–0 against
Leyton Orient. On 27 April 2013, Flynn secured promotion with Doncaster, and the
League One title, with a 1–0 win against
Brentford at
Griffin Park. Victory for Brentford would have seen them promoted at Doncaster's expense, and they were awarded a penalty-kick in injury-time, but missed and Doncaster scored from the resulting counterattack to earn the victory. At the end of the season, Flynn expressed a desire to step down as manager and return to a role of developing and recruiting players. Doncaster offered him a senior role in this as well as helping to choose the new manager. For the
2013–14 season he was named as
Director of Football including overseeing the newly formed
development squad which would be playing competitive games.
Return to Wrexham On 21 February 2019, Flynn returned to Wrexham as assistant manager to recently appointed manager
Bryan Hughes, who started his playing career at Wrexham under Flynn. ==Scouting career==