Southern said a fault with the 11:02 Brighton to London service came to a stand shortly after leaving Three Bridges station, which caused all the train between Brighton and Three Bridges to come to a stand as the line was blocked.
The driver called engineers to go through a series of fault finding procedures.
Southern said the service was terminated at Three Bridges and taken to the depot for further investigations and repairs.
A points failure also happened at Brighton earlier today.
Network Rail is working on fixing the points failure at Brighton, Southern said, and added that this is likely to mean more delays to services when approaching and leaving Brighton.
Passengers who are catching flights today from Gatwick Airport should allow extra time to complete the journey.
Disruption is expected to last for the rest of the day, Southern said.