This means no trains can run between the two stations.
The rail operator said the incident comes after a train hit a bird and then developed a fault.
A Southern spokesperson said: "We have been advised of the 14:23 Lewes to Brighton developing a fault just outside of Falmer station. The fault was caused by the train hitting a bird.
"When a train fault occurs, the driver will contact train technicians and will be guided through a repair process. If they are unable to fix the fault, the train will be terminated and taken out of passenger service and returned to the depot for full safety investigation and repairs. This is likely to have an immediate knock on effect, particularly in busy locations across our network, as well as on later services in the day.
"In this case the train fault could not be rectified. Therefore, a rescue train is required to attach and take the unit back to the depot. Until this process has been completed no services can run from Lewes to Brighton."
Southern said disruption is expected until 5pm.