He earned a new one-year contract in June 2009. In 2009–10 season he fell behind Stockdale in the pecking order, but eventually fought his way back to being Mark Schwarzer's back-up and was in the matchday squad for the Europa League Final. He had signed another one-year deal to remain at Craven Cottage, but was not picked for the team's Premier League squad for the 2010–11 season and faced an uncertain future at the club. On 1 July 2011, Fulham confirmed that Zuberbühler had left the club on a free transfer, after coming to the end of his contract.