No one was injured in the mishap near Tiruvalla station, which occurred at 3.55 AM, divisional railway sources said.
It was an air conditioned coach that went off the track, they said.
Some trains running in the Kochi-Thiruvananthapuram sector have since been diverted through Alappuzha.
Efforts are on to remove the derailed coach and traffic is expected to be restored before noon, sources said.