Thomson then had a short spell with Stenhousemuir during season 1996-97 making thirteen league appearances and scored no goals.
Queen of the South
Thomson first joined Dumfries club Queen of the South as the club were rebuilding in 1997 in the post Harkness era. New chairman Norman Blount was getting the wheels moving on the club's revival. In 1997 the club reached the Scottish Challenge Cup Final for the first time. Second Division Queens lost 1–0 to First Division Falkirk, despite a rousing Queens display at Motherwell's Fir Park, a performance that included the man of the match award going to Queens veteran central midfield playmaker Tommy Bryce and an early career appearance for Jamie McAllister. A late effort from Derek Townsley denied Queens an equaliser, as his gilt-edged chance went over the bar. Thomson made 65 league appearances during his first spell for Queens and scored 3 goals. In a later interview on the club website, reflecting on his time at Queens, McAllister listed Thomson among the best players that he played with at the club.
Arbroath
Thomson next went to Arbroath making 44 league appearances and scored 2 goals. He then followed in the footsteps of another distinguished player, Jimmy Binning, by leaving Arbroath to join Queen of the South. Thomson and his teammates ended the season in a promotion spot in the league.
Return to Queen of the South
He was 'player of the season' three times over a ten-year period for the Dumfries club. In late August and early September 2006 Thomson had a 'clean up' operation on his knee but came back successfully, including scoring with an overhead kick. Thomson made his 300th Queens appearance on 20 October 2007 in a First Division match against St Johnstone and is one of the select players to have made more than 300 appearances for Queen of the South. Thomson captained Queens during the 2007–08 Scottish Cup 4–3 semi-final victory against Aberdeen ; he was the first man to captain Queens in a Scottish Cup semi-final victory. As well as captaining the side in the final, Thomson also scored Queens' equaliser to bring the game against Rangers to 2–2. Despite Queens' battling second half display, Rangers eventually ran out 3–2 winners. As Scottish Cup runners-up, Queens qualified for the 2008–09 UEFA Cup. Thomson captained the team in their second qualification round games against Danish side FC Nordsjaelland. When Tommy Bryce was interviewed for the Queen of the South website, he named Thomson as being among the best players he had played beside at Queens. Thomson was also commended for his efforts when Andrew Coltart was interviewed for the club website. Thomson was given a testimonial by Queens on 18 July 2010. The result was a 1–0 win for Rangers. Thomson was retained as a player for the 2009–10 season after making 358 first team appearances and scoring a dozen goals. Thomson is 11th in the club's all time appearances list and also coached the under-19s team for the 2010–11 season. In his second spell at Queens, Thomson made 242 league appearances and scored 7 goals. Thomson overall played in 307 league matches and scored 10 league goals in his combined spells in Dumfries.
Career after playing
Thomson was appointed commercial manager at Queens on 1 June 2011, succeeding Mark McMinn. Thomson was appointed football development manager during May 2016. After Gavin Skelton left the club in November 2016, Thomson was appointed caretaker manager. Thomson reverted to his club role as football development manager after Gary Naysmith was appointed manager on 1 December 2016, alongside his assistant Dougie Anderson. In the summer of 2018, Thomson was appointed team manager of his hometown club, Kilsyth Rangers.
