Citing his disappointment at failing to gain promotion, Stimson resigned from his post at Grays on 16 May 2006. 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.