Frei was traded to Seattle Sounders FC on 10 December 2013 in exchange for a conditional pick in the 2015 MLS SuperDraft.

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."

Throughout the 2017 MLS season, Frei confirmed himself as one of the league's best goalkeepers once again: he started 33 games throughout the regular season, making 84 saves over the course of the year for a 69.4 per cent save percentage, and averaging 1.09 goals against per game, while also managing to keep 13 clean sheets, more than any other goalkeeper.
In the Playoffs, Frei only made four saves en route to the MLS Cup final, but kept four consecutive clean sheets, as Seattle reached the final without conceding a goal.
On 9 December 2017 he started in the 2017 MLS Cup Final against his former club Toronto FC at BMO Field, a rematch of the previous season's final; Toronto won the match 2–0 to complete an unprecedented treble of the MLS Cup, the Supporters' Shield, and the Canadian Championship, but Frei drew praise in the media for his performance throughout the match, following a string of impressive saves to keep the score level at half time, and made nine stops overall within the first hour of play.

On 10 November 2019, Frei started for Seattle in the 2019 MLS Cup Final, which ended in a 3–1 home win over Toronto FC.
Frei was traded to Seattle Sounders FC on 10 December 2013 in exchange for a conditional pick in the 2015 MLS SuperDraft.
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."
Throughout the 2017 MLS season, Frei confirmed himself as one of the league's best goalkeepers once again: he started 33 games throughout the regular season, making 84 saves over the course of the year for a 69.4 per cent save percentage, and averaging 1.09 goals against per game, while also managing to keep 13 clean sheets, more than any other goalkeeper. In the Playoffs, Frei only made four saves en route to the MLS Cup final, but kept four consecutive clean sheets, as Seattle reached the final without conceding a goal. On 9 December 2017 he started in the 2017 MLS Cup Final against his former club Toronto FC at BMO Field, a rematch of the previous season's final; Toronto won the match 2–0 to complete an unprecedented treble of the MLS Cup, the Supporters' Shield, and the Canadian Championship, but Frei drew praise in the media for his performance throughout the match, following a string of impressive saves to keep the score level at half time, and made nine stops overall within the first hour of play.
On 10 November 2019, Frei started for Seattle in the 2019 MLS Cup Final, which ended in a 3–1 home win over Toronto FC.
Stefan Frei