The 2016 Toronto FC II season was the second season in the club's history.

In 2015 the team finished 11th in the Eastern Conference, therefore, missing the playoffs.

[1] The squad of Toronto FC II will be composed of an unrestricted number of first-team players on loan to the reserve team, players signed to TFC II, and TFC Academy players.

Academy players who appear in matches with TFC II will retain their college eligibility.

Includes all competitive matches.