Frei was one of the best goalkeepers in the league during the 2016 MLS Season, keeping eight clean-sheets in 33 appearances (the joint fourth-most kept by a goalkeeper that season), as Seattle qualified for the playoffs after finishing fourth in the Western Conference. He only conceded three goals in the MLS Cup playoffs, keeping four clean sheets in six postseason matches. Frei was named MLS Cup 2016 MVP after making seven saves in regular play, and another in the 5–4 penalty shoot-out victory in the final against his former club, Toronto, following a 0–0 draw after extra-time; his decisive save on Jozy Altidore's header in the second half of extra-time was later described by the MLSSoccer.com reporter Sam Stejskal as "one of the best saves in MLS Cup history."