Southend United then offered £250,000 and a deal was agreed between the two clubs that led to Thomson leaving for Essex on 4 July 1994 to join Peter Taylor's Shrimpers [4] at Roots Hall.
[3][7] On 28 May 2000, Thomson scored the winning goal for Gillingham in the Football League Second Division play-off final at Wembley Stadium.
Following Ty Gooden's centre from the left, the diving Thomson stole in front of Stuart Balmer to glance the ball into the far corner of the net.
[3] Thomson also scored four goals in consecutive rounds of Gillingham's 1999–2000 FA Cup run, versus Cheltenham Town, Walsall, Bradford City and Sheffield Wednesday.
[9] The "Gills" were knocked out of the FA Cup in the quarter finals, the first time they had ever reached so far, at Stamford Bridge, when they lost 5–0 to Chelsea.
Thomson then signed on a free transfer for Queens Park Rangers on 22 March 2001 and stayed at Loftus Road until the end of the 2002–03 season.
[10] During his time with the London side Thomson featured as a 60th minute substitute in the 1–0 loss in the 2003 Football League Second Division play-off final to Cardiff City.
Thomson said on his return to Queens, "Things have changed quite a bit while I've been away – a new stand, a completely new set-up and a more modern type of training system".
Thomson then joined Stenhousemuir for the 2007–08 season, where he scored 5 goals in 18 league appearances until he was troubled by injuries and was forced to announce his retirement to the media on 18 March 2008.