On 13 September 2010, Flynn was confirmed caretaker manager of the Wales national football team after John Toshack stepped down, prior to the appointment of Gary Speed.
[8] 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.
[9][10] 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.
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.
[15][16] 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.
[20] 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.
[21] For the 2013–14 season he was named as Director of Football[22] including overseeing the newly formed development squad[23] which would be playing competitive games.