He began his professional career at the local Swiss club FC Basel, playing four seasons in the first team before moving to Borussia Dortmund. He spent three years at the German club, his last season being marred by injury. Degen signed for Liverpool on a free transfer on 3 July 2008, his stay at Liverpool was also blemished by many injuries. His Liverpool contract was terminated by mutual consent on 31 August 2011 and he returned to Basel. Degen ended his professional career at the end of season 2015/16 with a total of eight Swiss championship titles.