On 16 June 2009, Kelly signed a three-year contract with Fulham, making him the club's first signing of the 2009 summer window. He said he was delighted to join the Cottagers and was looking forward to representing the club in both the Premier League and Europa League. He helped Fulham reach the 2010 UEFA Europa League Final, playing in their memorable win against Juventus on the way, but he was left out of the squad for the final itself.