However, he came through the ranks with FC Basel, joining their youth department and playing in their U-16 team, winning the Swiss championship title for that age group in the 2004–05 season.

[5] The team won their division and became Swiss champions at U-21 level, Frei, playing as attacking midfielder, made 30 appearances, scoring 11 goals.

[6] Ahead of their 2007–08 season Frei was called into the first team squad by head coach Christian Gross.

[8] He played his UEFA Cup debut with the team in the home game on 16 August, coming on as substitute, as Basel won 2–1 against SV Mattersburg.

Winning both matches in the qualification round and both matches in the play-off round, they team advanced to the group stage, which they ended undefeated in second position, after playing 1–0 at home against Stade Rennes, 0–0 away against Dinamo Zagreb, 1–0 at home against Brann and 1–1 away against Hamburger SV, to continue the knockout stage.

[13] Frei played his UEFA Champions League debut for Basel on 26 November 2008 in the 5–0 away defeat against Shakhtar Donetsk.

Frei scored his first Champions League goal for Basel on 14 September 2011 in the Group C 2–1 home win against Oțelul Galați,[16] his second on 27 September in the 3–3 draw at Old Trafford against Manchester United[17] and his third on 22 November in the Arena Națională, in Bucharest, as Basel won the away game against Oțelul Galați 3–2.

[18] At the end of the 2011–12 season, Frei won the Double, the League Championship title[19] and the Swiss Cup[20] with Basel.

The championship was won for the sixth time in a row that season[26] and in the 2014–15 Swiss Cup they reached the final.

Basel entered the Champions League in the group stage and reached the knockout phase as on 9 December 2014 they managed a 1–1 draw at Anfield against Liverpool.

[29] On 23 December 2017, FC Basel announced that Frei would return to the club, signing a four-and-a-half-year contract dated up until June 2022.

On the final day of the summer 2024 transfer window, FCB announced that their captain Fabian Frei had decided to rejoin his youth club Winterthur.

[33] On the day of his departure from Basel, he joined fellow Super League side FC Winterthur.

Frei gave his international debut for Switzerland on 7 October 2011 in the UEFA Euro 2012 qualifying game in the Liberty Stadium against Wales.

Frei was selected to represent Switzerland in the men's football tournament at the 2012 Summer Olympics as part of the Swiss under-23 team.