Southern Rail confirmed Network Rail response teams had moved the tree but warned services may still be subject to delay, cancellation and alteration.
The incident happened at Ifield, a spokesman said.
In a separate incident the line running from Holmwood towards Horsham is blocked due to a train hitting an obstruction, according to Southern.
The spokesman said: “Engineers and the train crew are investigating the situation and working to move the train as quickly as possible.
“Train services running through this station may be delayed or revised.”
Ticket acceptance is in place.