Thompson followed his brother Albert and joined the Wanderers, for whom he made his first appearance on 14 February 1872 in a 6–1 victory over the Civil Service. Despite having only played one other match for them, he was selected for the Wanderers in their defence of the FA Cup in the 1873 FA Cup Final played at Lillie Bridge on 29 March 1873. In the final, the Wanderers defeated Oxford University 2–0, with goals from Arthur Kinnaird and Charles Wollaston.