Bundesliga, Borussia manager Jos Luhukay loaned him out to his former club, Basel for the 2007–08 season.

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.

[3] 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.

[7] They also reached the final of the 2013–14 Swiss Cup, but were beaten 2–0 by Zürich after extra time.