Southwest spokesman Chris Mainz said Tuesday that the Philadelphia-Boston route "just hasn't performed the way that we would have liked."
"With the current economic environment, fuel prices, we are having to make some hard decisions with regard to flights and routes," he said.
Southwest has been retreating in Philadelphia, from a peak of 71 flights to 20 cities, to 55 flights to 18 destinations currently.
In July, Southwest announced it would eliminate four of those destinations on Jan. 8: Pittsburgh; Providence, R.I.; Manchester, N.H.; and Jacksonville, Fla.
At the time, Southwest also said it would trim Philadelphia-to-Boston flights from eight a day to six, then to five in February. But there was no mention of its pulling out of the route altogether.
The Dallas-based low-cost airline - which recently acquired the smaller AirTran Airways - is expanding in cities including Atlanta and Denver. In Philadelphia, US Airways, with an international hub and 444 daily flights, has proved to be a tough competitor, with fares that often beat Southwest's ticket prices.
"Obviously, Southwest sees a bunch of opportunities around the AirTran acquisition," said airline analyst Bob McAdoo, of Avondale Partners L.L.C.
The competitive situation in Denver, where United Airlines is pulling back, and in Atlanta, where AirTran is strong, may look "more attractive than continuing to grind out marginal returns in Philadelphia against US Airways, which has been a very strong, very dedicated competitor," McAdoo said.
He speculated that low-fare JetBlue Airways, with 100 daily flights from Boston - that city's largest carrier - may now come here.