After playing for Clyde he won the 1954–55 Football League with Chelsea and the 1959 FA Cup Final with Nottingham Forest.

Thomson was a member of Chelsea's 1954–55 league title-winning side playing in the final 16 games of the run-in.

That included the title decider against Chelsea's main rivals, Wolverhampton Wanderers, in which Thomson made a crucial last-minute save to secure a 1–0 win.

Thomson made his debut for Forest in the opening game of the 1957/58 season at the City Ground in a 2–1 victory against Preston North End.

Luton Town hit back midway through the second half after Forest's opening goalscorer Roy Dwight broke his leg in the 33rd minute.