The derailment took place in the early hours at Norwood Junction.
London Overground services were suspended this morning between Sydenham and West Croydon and there was no service on Southern trains between Norwood Junction and West Croydon, Sutton and Epsom.
Network Rail said engineers attended and normal service was resumed at midday, with some delays possible.
A spokesman said the derailed train was put back on the tracks and engineers checked the rails.