After a transfer to French club Rennes, he finished as the highest goal-scorer in Ligue 1 for the 2004–05 season with 20 goals.

[3] On 17 July 2009, he left Borussia Dortmund after 74 league matches[4] and, after six years, returned to Switzerland to sign with FC Basel.

At the end of the 2011–12 season, Frei won his second Double with Basel, the League Championship title[7] and the Swiss Cup.

Frei played his last professional match on 14 April 2013 in the home game at St. Jakob-Park as Basel beat Zürich 3–1.

Frei played his debut as full international on 24 March 2001,[15] being substituted in, during the 1–1 away draw against the Republic of Yugoslavia during the World Cup qualification Group 1 match.

[18] He scored six times in 2006 FIFA World Cup qualification, including a second-minute penalty in the second leg of the play-off against Turkey which his team won on away goals.

[19] At the finals in Germany, Frei was Man of the match in the 2–0 group stage win over Togo in Dortmund, opening the scoring from Tranquillo Barnetta's 17th-minute cross.

[20] He concluded a win by the same score against South Korea in the next game to send Switzerland through as group winners.

[21] On 30 May 2008, in Switzerland's final preparation match before co-hosting UEFA Euro 2008, Frei scored twice in a 3–0 friendly win over Liechtenstein.

[24] On 5 April 2011, he decided to quit from the national squad after being criticised again following a 0–0 draw with Bulgaria on 26 March for the Euro 2012 qualifying match.

[30][31] After successfully leading Winterthur to promotion to the Super League, he was signed by his former club FC Basel to be their new head coach.

[32] Frei and Basel parted ways on 7 February 2023, with the team sitting in seventh place in the table.

[33] According to FC Basel sporting director Heiko Vogel the 0–1 loss away to Grasshopper Club Zürich, following five league games without a win, on 4 February 2023, three days before, "was one defeat too many".

[36] However, he is the second-cousin of Seattle Sounders FC goalkeeper and former Swiss youth international Stefan Frei.