In October 2021, Thomson was signed by the BC Lions of the Canadian Football League (CFL). He appeared in two games during the 2021 season as the third string but recorded no statistics. In , Thomson battled Michael O'Connor for the second-string quarterback spot. He was said to have impressed the team, but suffered a serious injury in preseason on a controversial hit by Titus Wall and was released after dressing in only one game as the Lions signed Antonio Pipkin to be the third string quarterback.
