On 31 August 2011, Liverpool announced the release of Degen. Just a short time later, he made the request to the then Basel manager Thorsten Fink if he could keep fit with his home club's first team. Fink left the club in October 2011 and the new manager Heiko Vogel offered him a contract on 20 November 2011. Following his return he played his first game in the 2011 Swiss Cup tie against FC Wil. He scored the equaliser to 2–2 as Basel won 3–2 aet. He played is first league match in St. Jakob Park on 3 December 2011 in the 1–0 home victory against FC Luzern. At the end of the 2011–12 season, Degen won the Double, the League Championship title and the Swiss Cup with Basel.