On 22 June 2005, he was appointed as the first ever manager of
FC United of Manchester after one of their players, Joz Mitten, recommended him to the board and led the team to immediate success by achieving promotion in each of their first three seasons. The club currently play in the
National League North, the sixth tier of English football, after gaining promotion in the 2014–15 season by winning the
Northern Premier League Premier Division title. In the 2010–11 season, Marginson led them into the
FA Cup proper for the first time, where they upset
Rochdale to reach the second round. Marginson is regularly celebrated by fans of the club at matches, home and away, due to these achievements. For the first five seasons, he led the club on a semi-professional basis but later gave up his fruit and vegetable delivery business to work full-time for FC United, a role which included involvement in the club's community work such as coaching youngsters and other groups. On 24 October 2017, Marginson left his post as manager at F.C. United by mutual agreement. In November 2018, he was appointed Head of Football Operations at
Radcliffe F.C. In October 2023, he was appointed manager of
Trafford Football Club. == Managerial statistics ==