[4] Thomson earned an unexpectedly early debut in March 2005, when a flu epidemic at Tynecastle forced Hearts' head coach John Robertson into naming a plethora of youngsters in his first team squad against Inverness Caledonian Thistle.

It was a different story in 2005–06 however, as a wave of new signings and Hearts' impressive form ensured Thomson spent the entire season playing reserve and under-19 football.

[14][15] He made his debut on the opening day of the season against St Mirren at East End Park[16] and scored his first goal for the club against Kilmarnock on 10 September.

[18] Thomson admitted he would be happy to make his loan deal permanent as he was delighted to be playing regular first team football.

[23] On 2 March 2012, Thomson joined Scottish First Division side Raith Rovers on loan until the end of the season.

[26][27] On 6 April 2014, Thomson captained Raith Rovers as they defeated Rangers 1–0 at Easter Road to win the Scottish Challenge Cup.

[31] Thomson signed for Kelty Hearts in September 2022[32] and extended his contract with the club at the end of the season.