Josh Bailey and Mathew Barzal scored in the third period for the Islanders (3-4-2), who came back from 3-1 but lost their fifth in a row (0-3-2). Nick Leddy also scored, and Ilya Sorokin made 25 saves.
Sorokin has lost his first three NHL starts, allowing 11 goals.
"I'm taking the positive out of it," New York coach Barry Trotz said. "We're sitting there after two periods and [with] the way the week has gone, we could've just said, 'Let's get out of here,' and give up. We didn't. We battled back. I thought they uplifted each other. I felt we were going to get two points, I really did."
New York's comeback started with Bailey's first goal of the season at 1:03 of the third period to make it 3-2.
Barzal tied it 3-3 at 6:27 with a one-timer off the rush after Anders Lee outraced Flyers defenseman Justin Braun to the puck in the corner and delivered a pass to the Islanders center in between the hash marks.
"We had a pretty good response to find a way to tie that game up," Lee said. "It wasn't as complete game as we would have liked, but at the end of the day we climb out of a hole that we dug ourselves in and found ourselves with an opportunity to get that second point."