The winger picked up the problem in a tackle after just 20 minutes at Craven Cottage.
It was a cruel blow for the Irish international who was back in the starting line-up for the first time since suffering the same injury at Middlesbrough in December.
Head Coach Martin Jol confirmed: Ã¢â‚¬Å“He has the same injury as before, a medial ligament problem and it seems to be worse, so heÃ¢â‚¬â„¢ll be out for four to six weeks. ThatÃ¢â‚¬â„¢s a big disappointment.Ã¢â‚¬Â
Andy Reid is facing up to six weeks on the sidelines after suffering a knee ligament injury at Fulham on Tuesday night.