No injuries were reported but service was expected to be hampered for hours on the railroad's Harlem line.
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Railroad spokesman Aaron Donovan says the Manhattan-bound train hit the tree around noon north of the Hawthorne station in Westchester County.
There were about 100 passengers on the six-car train. They were put on another train on an adjacent track.
Crews are working to re-rail that set of wheels and inspect and repair a stretch of about 100 feet of track that was damaged in the incident.
The railroad is operating on reduced capacity between North White Plains and Mt. Kisco, but expects the Harlem Line to return to regular schedule Tuesday.
Harlem Line tickets are being cross-honored on the Hudson & New Haven Lines.
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There were numerous reports of fallen trees in the metropolitan area on Monday and forecasters were warning of high winds.
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