The Republic of Ireland international has now tied himself to the West London outfit until 2013.
"I’ve enjoyed every minute of my time at Fulham since joining two years ago and I’m delighted to be staying at the Cottage until at least 2013," the 30-year-old told the club's official website.
"This is a fantastic club with great supporters and it’s a very exciting time to be part of the team. I feel in great condition and I’m hungry to achieve more success for this club."
"We’ve had some great moments together so far and I believe there’s more to come from us in the Premier League and Europe this season under Martin Jol," he added.
Duff joined Fulham from Newcastle United in 2009 for an undisclosed fee.