He enrolled at the University of Michigan in 1909 as a special student. In November 1910, the
University of Minnesota challenged Thomson's eligibility to play against the Golden Gophers in the final game of the season. The dean of Michigan's literary department was deputized to investigate. The investigation concluded that Thomson's entrance credits were "equivalent to the requirements of the literary department, though not corresponding to the precise subjects enumerated in the university calendar." As a junior, Thomson was the high scorer on the
1911 Michigan Wolverines football team with seven touchdowns in seven games for a total of 35 points. Thomson started seven of eight games in 1911. His brother died two days before the Penn game, and Thomson returned home to
Cadillac, Michigan to be with his family. When it was announced the Thomson would not play against Penn,
The New York Times reported: "The announcement caused heavy gloom to spread through university circles, as it was said that Thompson's [sic] absence would remove the pivot of Michigan's offensive and defensive strength." At the end of the 1911 season, Thomson was selected as the first-team All-Western fullback both by
Walter Eckersall in the
Chicago Daily Tribune and by E. C. Patterson in ''
Collier's Weekly''. At the end of November 1911, the
varsity letter winners from Michigan's 1911 team unanimously elected Thomson as the captain of the
1912 Michigan Wolverines football team. Under Thomson's captaincy, the 1912 team compiled a 5–2 record. Michigan's head coach Fielding H. Yost praised Thomson's performance against Cornell and called it Thomson's best effort. Yost also named Thomson to his 1912 All-Western team. Thomson was a member of the
Alpha Delta Phi fraternity at Michigan. He graduated from Michigan with a bachelor of law degree in 1913. ==Later years==