He was appointed manager of Grays Athletic in 2002 and remained in charge until 2006 when he took over as manager of Stevenage Borough. He led Grays to victory in the Final of the FA Trophy in 2005 and 2006, and repeated the feat with Stevenage in 2007. In November 2007, he became manager of a Football League team for the first time when he took over at one of his former clubs, Gillingham, but he was unable to prevent the club's relegation from League One at the end of the 2007–08 season. He led Gillingham back into League One the following season via the League Two play-off Final, but his contract was terminated after the team were relegated back to League Two the following season. On 1 June 2010, Stimson was appointed as the new manager of League Two club Barnet, but he was sacked on New Year's Day 2011 with the club near the bottom of the table. He later had a spell as manager with Conference club Kettering Town.