Born in Geneva, Vogel joined Swiss amateur club FC Meyrin in his youth, but made the cut into professional football by joining Grasshopper Club Zürich. In his time at Grasshoppers, he usually played central defence or rightback although on occasion, he could be called to feature in a central defensive midfield role. In his role as a defensive midfield player, in which he uses his ability to pass accurately and to effectively retain possession of the ball, Vogel can be counted on to add depth to either defence or attack.
PSV and Milan
Dutch club PSV sought his services in 1999 and he became a prominent member of the team until he decided to leave to join Milan at the end of the 2004–05 season. In his final season with PSV, he was noted for forming a formidable midfield partnership with Mark van Bommel and Phillip Cocu where the club managed to reach the semi-finals of the Champions League tournament.
On 31 August 2006, he joined Real Betis in an exchange deal for Ricardo Oliveira. Vogel made his Betis debut against Athletic Bilbao on 10 September 2006 at the Manuel Ruiz de Lopera, which Betis won 3–0. Vogel made his last La Liga appearance for Betis on 19 May 2007 against Tarragona. On 27 December 2007, he agreed to leave Betis after suing them. Everton confirmed they were in talks to sign the player after being told he could leave his then club Real Betis in July 2007. However the deal hit problems due to Real Betis wanting payment for him.
Blackburn Rovers
On 18 March 2008, he agreed a two and a half year contract with Mark Hughes' Blackburn Rovers. Vogel joined fellow Swiss footballers Stéphane Henchoz and Bruno Berner at Ewood Park, as well as his former PSV-colleague André Ooijer. After receiving International clearance to play for Blackburn Rovers on 25 March, he was given the number 8 shirt by Mark Hughes, the shirt vacated by Robbie Savage after his move to Derby County. Vogel made his debut for Rovers on 5 April against Tottenham Hotspur. However, in the 2008–09 season, Vogel found himself frozen out at Ewood Park. He came on as a substitute in a 3–1 defeat by Liverpool. On 7 April 2009, his contract was terminated by Blackburn Rovers with immediate effect and by mutual consent. After that, he announced his retirement from professional football.
Grasshoppers comeback
Two and a half years after his retirement, Vogel decided to return to the field again. He made comeback with Grasshoppers where he made his professional debut and appeared in the starting line-up against FC Thun on 5 February 2012. After appearing in another two league matches, he retired for the second time.