As manager Flemming Serritslev ensured Danish side B1909 a place in the best Danish league in 1990. In 1992, he became assistant manager of the Danish national team before he went on to become head coach of the Danish U21 team. In 2006 Serritslev returned to his childhood club Vejle as sports manager. However, Serritslev and the new board at the club could not work together and Serritslev left Vejle Boldklub only six-month after his appointment.[1]
On 1 July 2010, he was appointed as technical manager of Mes Kerman in Iran Pro League and also head coach of Mes B. On 25 August 2011, after the resignation of Mes head coach Samad Marfavi, he was appointed as caretaker manager of club but was replaced with Miroslav Blažević without managing team in any match.[2]