With his current deal set to expire next summer, the Northern Ireland international has signed a new deal to remain at Craven Cottage until the end of the 2013-2014 season
Hughes has racked up over 200 games for the Cottagers since his transfer from Aston Villa, and manager Martin Jol was keen to tie him down to avoid his man being able to talk to other clubs from January onwards.
"I'm obviously delighted as I've enjoyed my time here so far," Hughes told the official club website. "To know I'll be around for another couple of years is a nice thing for me.
"When I signed for Fulham, I didn't know how long I'd be here for, I just wanted to do well and fit into the team.
"I've had lots of good experiences so far and hopefully there'll be many more between now and 2014."
The news of Hughes' deal with the club is their second contractual boost this week, following the arrival of Greek international midfielder Giorgos Karagounis on a free-transfer from Panathinaikos.