Thomson scored his second goal of the 2008–09 season when he scored an equalising goal in injury time against Dundee United at Ibrox Stadium, on 4 November 2008. In the following league match against Kilmarnock at Rugby Park, a 4–0 victory for Rangers was overshadowed by Thomson suffering a serious knee injury. This injury ruled him out for the rest of the 2008–09 season. Thomson had surgery to save his career on 31 December 2008. The surgery was a success and Thomson hoped to be fit for the following season. On his return to the Rangers first team, Thomson was sent off in the 13th minute of a 2–1 win against Hearts.