Travis Konecny and Joel Farabee also scored, and Morgan Frost had two assists for the Flyers. Samuel Ersson made 13 saves.
Morgan Geekie scored, and Jeremy Swayman made 21 saves for the Bruins.
Geekie gave Boston a 1-0 lead at 14:50 of the first period with a power-play goal.
Atkinson tied it 1-1 at 1:10 of the second period, scoring with a backhand in front.
Konecny scored 58 seconds later at 2:08 to give Philadelphia a 2-1 lead, and Farabee extended it to 3-1 at 16:00.
