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.