The first was reported just after 7:30 a.m. in Wilton, Metro-North said in a social media post.
None of the 70 people on board were injured, and rail authorities moved all passengers to buses to complete their trips. Service has since returned to normal.
Several hours later, it happened again in New York.
A northbound Harlem Line train hit a tree near Hawthorne hours after the first tree strike.
The southbound Harlem Line service between North White Plains and Hawthorne resumed just before noon. Northbound customers looking to travel to those stations should take a southbound train from Pleasantville, Metro-North said on X.
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