At the end of the 1988–89 season, Stimson was transferred to Newcastle United, then in the Second Division, for a fee of £200,000. He spent four years with the club and finally gained a regular first team place, making over 80 appearances. After Kevin Keegan took over as manager, however, Stimson found himself out of favour and he had a short spell on loan to Portsmouth in December 1992, which led to a £100,000 transfer at the end of that season. He made over fifty appearances for Portsmouth but was also loaned out again, this time to Barnet during the early part of the 1995–96 season. In March 1996, he was transferred to Southend United for a fee of £25,000. His first season at the club was affected by a long lay-off due to injury, meaning that he did not play between August and November, but he ultimately made over 50 Football League appearances for the club. During his time at Roots Hall the club suffered two consecutive relegations, dropping from the First Division into the Second Division in 1997 and from there into the Third Division in 1998. In March 1999, having not played for Southend since the previous November, he returned to former club Leyton Orient on a free transfer. He played for the club in the semi-finals of the play-offs, but was restricted to an appearance as an unused substitute in the final, which Orient lost.