Four SEPTA workers were onboard when the incident happened around 10:00 p.m. on the Media Elwyn Line.
The train was heading towards Philadelphia when the tree fell and damaged two of the electrical connectors on the roof of the train, officials say.
Service was stopped for several hours while crews made repairs and cleared the tree.
SEPTA officials say everything was back to normal around 7:15 a.m. Thursday.
