It was New York's first win over the Flyers in 16 tries. The Islanders built a 4-0 lead and withstood a late charge to defeat Philadelphia for the first time since Feb. 12, 2008.
Philadelphia remained part of a tie with Montreal and Boston for the last three playoff positions in the Eastern Conference. Those teams have a two-point lead over Atlanta which, like the Flyers and Bruins, suffered a loss Thursday.
Martin Biron stopped 31-of-35 shots, but allowed late goals by Danny Briere and Darroll Powe to make the game interesting.
The Islanders, who are third from the bottom in the conference, won for the third time in four games.
Brian Boucher allowed five goals on 24 shots before being removed in the third period. Jeremy Duchesne then made his NHL debut and stopped three shots.