On 27 June 2007, Hughes was announced as a new signing for Premier League side Fulham. He was quoted as saying "I'm delighted to be joining Fulham and am looking forward to working with Lawrie Sanchez at club level. I enjoyed my time at Aston Villa but when this opportunity presented itself I had no hesitation in coming to discuss the Manager's ambitions for the Club, which obviously were of great interest to me. I'm happy to have signed before the start of pre-season, which gives me the opportunity of being with the lads on day one, when we come back to training next week." He took the captain's armband in the absence of Brian McBride and latterly, Danny Murphy. On 4 December 2009, Hughes signed a new deal with the club which would see him remain at Craven Cottage until the summer of 2013.