In September 2002, Stimson took over as manager of Grays after the sacking of Craig Edwards, initially as
caretaker manager, but after leading the team to its first victory of the season, he was quickly given the job on an ongoing basis. Despite the signing of a number of former top-level players, such as
Carl Leaburn and
Jason Dozzell, the team escaped relegation by only one point. The following season, however, boosted by a switch to full-time professional status and helped by the goals of
Freddy Eastwood, Grays finished in 6th place, thus achieving promotion to the
Conference National, the top level of
non-league football, for the first time in their history. In the same season, Stimson also led Grays to the FA Trophy Final, where the team beat
Hucknall Town in a
penalty shoot-out. Grays reached the FA Trophy Final again in the following season, and claimed a second successive win after a 2–0 victory over
Woking at
Upton Park. In the Conference, Grays finished in third place and qualified for the play-offs for
promotion to
the Football League, but lost to
Halifax Town in the semi-finals. He stated that at the time he had received no firm job offers from other clubs, and acknowledged that he was taking a gamble with his career, but said that if he was unable to find a new job as a manager he would move into youth coaching or open his own football school. He was linked with the managerial vacancy at
League Two Peterborough United, but eventually took over as manager of
Stevenage Borough on 28 May, and led the club to an eighth-place finish in the Conference National in his first season in charge. Stevenage also defeated Stimson's former club Grays to reach the FA Trophy final, and beat
Kidderminster Harriers 3–2 at the new
Wembley Stadium in the final, giving Stimson a third consecutive Trophy win as a manager. match in 2008 In the early part of the
2007–08 season, speculation began to mount that Stimson would be approached to take over as manager of a Football League club, with Gillingham,
Port Vale and
Millwall all alleged to be interested in his services. He was offered a new contract by Stevenage on 16 October 2007, but resigned the following day. On 1 November, he was appointed as the new manager of Gillingham, and quickly moved to sign a number of Stevenage players, including
Adam Miller and
John Nutter. He was unable to recreate his previous success, however, and at the end of the 2007–08 season Gillingham were relegated from
League One. He was also criticised by departing player
Aaron Brown, who acknowledged that Stimson had strong coaching skills but described his man-management as "shocking". The following season the Gills finished fifth in League Two and beat
Shrewsbury Town 1–0 in the
play-off final at
Wembley Stadium to gain promotion, but in the
2009–10 season Gillingham were relegated back to League Two, after which Stimson's contract was terminated "by mutual consent" on 10 May 2010. On 1 June, Stimson was appointed as the new manager of League Two club
Barnet, but was sacked seven months later on 1 January 2011 due to a bad string of results which left the club near the bottom of the table. Towards the latter stages of the 2010–11 season, Stimson accepted a coaching role at
Dagenham & Redbridge. After a brief spell at Dagenham, he was appointed manager of
Conference National club
Kettering Town on 7 September 2011. On 4 January 2012, Stimson left Kettering with the team placed in the Conference relegation places. Four months later he was appointed manager of
Thurrock following the club's relegation to the
Isthmian League. At the age of 49, Stimson was registered as a player again for the 2017–18 season and named himself as a substitute on a number of occasions. On 10 May 2018, after leaving Thurrock as a result of the club folding, Stimson was appointed manager of
Waltham Abbey. In November of the same year, however, he resigned in order to take over as manager of
AFC Hornchurch. He led the club to the
2021 FA Trophy Final at
Wembley Stadium, beating
Hereford 3–1. After leaving Hornchurch at the end of the
2022–23 season, Stimson returned to
Grays Athletic for the upcoming season, but he was sacked in November with the club lying second from bottom in the
Isthmian League North Division. The following month he was appointed manager of
Margate. Having been unable to prevent the club from being relegated, Stimson was dismissed from his role at the end of the season. In April 2025, Stimson was appointed assistant manager of Isthmian League Premier Division side
Cray Wanderers for the 2025–26 season. ==Personal life==