Network Rail engineers are investigating the fault, which was first reported at 11.37am this morning (June 19).
Services running through Brighton, Haywards Heath, Three Bridges and Gatwick Airport may be cancelled or delayed by up to 45 minutes, Southern said.
Disruption is expected until 3pm this afternoon.
A Statement from Southern Rail said: “Due to a fault with the electricity supply to the signalling equipment in the Balcombe area, services are subject to delay and alteration.
“Network Rail, who own and maintain the signalling and track, are attending the reported signalling fault and will be providing updates to us. They are expected to be on site at shortly and we will then provide further information about the problem.
“Trains are having to stop and speak to the signal man to gain authority to proceed between Balcombe and Haywards Heath in both directions
“This is affecting Gatwick Express, Southern and Thameslink services.”