On March 24, Thole was reassigned to minor league camp and started the season with the Triple-A Buffalo Bisons. He was recalled by the Blue Jays on June 7 when Henry Blanco was designated for assignment. Thole made his Blue Jays debut in the 16th inning of an 18 inning win against the Texas Rangers on June 8, going 0-2 at the plate. He finished the 2013 season batting just .175 with one home run and eight RBI in 45 games. Thole began the 2014 season in Toronto, as R. A. Dickey's personal catcher. He improved upon his results from 2013, finishing 2014 with a batting average of .252 with 7 RBI in 56 games played. On November 1, the Blue Jays picked up Thole's $1.75 million option for the 2015 season.
