Degen started his youth football with local club FC Oberdorf. In 1996, he transferred to the youth teams of
FC Basel playing in their U-18 and U-21 teams. He started his professional career at
FC Aarau in 2000 but returned to Basel in 2003. With the club, during the
Super League season 2003–04 and
2004–05, Degen won two domestic league titles. Degen moved to
Bundesliga club
Borussia Mönchengladbach in 2006. He played his debut for Mönchengladbach on 14 October 2006 in the game against
VfL Wolfsburg and scored his first goal for his new club in that game. However, after the club's relegation in the
Bundesliga season 2006–07 into the
2. Bundesliga, Borussia manager
Jos Luhukay loaned him out to his former club, Basel for the 2007–08 season. On 22 August 2008, he returned to Switzerland on a permanent deal with
BSC Young Boys. Degen spent four seasons in Bern playing 106 league matches and scoring 17 goals. On 31 May 2012, Basel announced that they had signed Degen on a contract up until June 2015 together with his brother
Philipp. He started his first game for his team following his return against
Servette FC on 13 July and scored the winning goal to the 1–0 victory. At the end of the
Swiss Super League season 2012–13 Degen won the Championship title and was
Swiss Cup runner up with Basel. In the
2012–13 UEFA Europa League Basel advanced as far as the
semi-finals, there being matched against the reigning
UEFA Champions League holders
Chelsea, but were knocked out being beaten 2–5 on aggregate. At the end of the
2013–14 Super League season Degan won his fifth league championship with Basel. They also reached the final of the
2013–14 Swiss Cup, but were beaten 2–0 by
Zürich after extra time. In the
2013–14 Champions League season Basel in the
group stage finished the group in third position to qualify for
Europa League knockout phase and here they advanced as far as the quarter-finals. After the season Degen retired from professional football. ==International career==