After being cut by the Bills, prior to the start of the 2007 NFL season, Thompson signed with the Edmonton Eskimos of the Canadian Football League. He was on their negotiation list for 2 years prior to his signing. Thompson spent his first year in the CFL with the Eskimos.[6] He totaled 12 defensive tackles and one interception in that season.[6]
Hamilton Tiger-Cats
Thompson was traded from Edmonton
to the Hamilton Tiger-Cats on February 13, 2008.[6] In his second year in the CFL Thompson was named a CFL All-Star. He set career highs in tackles with 60 and interceptions with 9. The following year, which was the 2009 CFL season, Thompson accumulated 49 tackles and 1 interception.
Edmonton Eskimos (second stint)
Chris Thompson returned to the Eskimos for the 2010 CFL season. He would remain on the team for the next season through the 2013 CFL season. During those 4 seasons Thompson averaged 46.7 tackles per season and totaled 19 interceptions. Following the 2013 CFL season Thompson was released by the Eskimos on March 14, 2014.[8]
Montreal Alouettes
After not playing for the 2014 season, Thompson and the Montreal Alouettes agreed to a contract on February 20, 2015.[9] On June 9, 2015, it was reported by Herb Zurkousky of the Montreal Gazette that Thompson was released by the Alouettes.