Following the 2015 season, in February 2016, Irwin was traded to Toronto FC in exchange for targeted allocation money, a third-round pick in the 2016 MLS SuperDraft and a conditional first-round pick in the 2017 MLS SuperDraft. After featuring as the club's starting goalkeeper for the first part of the season, Irwin sustained in injury in July, and as a result, he was replaced by his deputy Alex Bono in the starting line-up by manager Greg Vanney; Upon his return to action, Irwin later regained the starting spot for the remainder of the regular season and the Playoffs, as Toronto went on to reach the 2016 MLS Cup Final. In the final, held at BMO Field on December 10, Toronto were defeated by the Seattle Sounders 5–4 on penalties, following a 0–0 draw after extra time; Irwin was able to stop Álvaro Fernández's spot kick during the shootout, but misses from teammates Michael Bradley and Justin Morrow ultimately proved to be decisive. On December 13, 2016, Irwin was selected by Atlanta United FC in the third round of the 2016 MLS Expansion Draft, but was immediately traded back to Toronto for Mark Bloom and allocation money.