Thomson joined Scottish Championship club Dumbarton in August 2016, for the first half of the season.[6] He scored his first senior goal in a 2–2 draw with Dunfermline Athletic on 29 October 2016.[7] Thomson departed the Sons on 31 December 2016, when his loan deal ended.[8]
On 1 January 2017, Thomson subsequently joined fellow Scottish Championship club Queen of the South for the second half of the season, scoring on his debut against St Mirren on 7 January 2017.[9] Thomson then returned to his parent club, Celtic at the end of the 2016–17 season.[10]
At the start of August 2017, Thomson was sent out on loan to Livingston for six months to gain first-team experience,[11] but was recalled back to his parent club in early September 2017, due to a disagreement between the clubs regarding the handling of the player, having only played three league matches for the West Lothian side.[citation needed]
On 29 December 2017, Thomson joined Queen of the South for a second spell on loan. He initially joined on an emergency loan deal, although he remained with the side until the end of the season.[12] On 20 March 2018, Thomson scored twice in the club's first league victory at Tannadice since 1933, in a 3–2 win versus Dundee United.[13]
Dunfermline Athletic
On 16 June 2018, Thomson signed for Scottish Championship club Dunfermline Athletic.[14][15] He made his debut starting in a 3–0 win versus Peterhead in the Scottish League Cup on 17 July 2018,[16] and scored his first goal in a league match against Dundee United on 4 August 2018.[17][18]
Thomson was voted Fans Player of the Year in his first season with Dunfermline. After missing part of his second season recovering from injury Thomson was released in May 2020 at the end of his contract along with 16 other players as COVID-19 impacted the clubs financial position.[19]
Derry City
In June 2020, Thomson joined League of Ireland club Derry City on an initial 18 months contract and he scored in his Europa League debut. In November 2021 after winning the previous season's Supporters Player of the Year award Thomsons contract was extended for another 2 years.
He was selected for the under-20 squad in the 2017 Toulon Tournament.[22] After a historic first ever win against Brazil, which was at any level.[23] Scotland later won the bronze medal.[24] It was the nations first ever medal at the competition.[25]