Thomson's time with Sunderland was no less successful than his time with Hearts. Quickly appointed club captain, he led the team through a remarkably consistent period: during his time with the club they finished no lower than eighth in the First Division. He made over 264 major appearances for Sunderland (7 goals) and helped them to the 1912–13 League title. The Black Cats narrowly missed out on a double that season when beaten 1–0 by Aston Villa in the 1913 FA Cup Final, with Thomson and the Villa centre-forward Harry Hampton both later suspended for a month for their conduct in what was a bruising occasion.