The blaze led to cancellations and delays during the morning with Virgin West Coast and Arriva Trains services disrupted.
No one was reported to have been injured in the fire which was in the diesel engine compartment of the train.
A Cheshire Fire and Rescue Service spokeswoman said: “At 4.03am, firefighters were called to reports of a train on fire on Station Road, Calveley.
“On arrival firefighters found a fire involving the diesel engine compartment of a train.
“They used three powder extinguishers, one hose reel jet, two breathing apparatus and a thermal imaging camera to extinguish the fire.
“Around 11am, one fire engine from Chester was called to assist with the recovery of the train.”
Fire investigators were reported to have been sent to the scene. It is unclear which railway company operated the train involved.
A National Rail spokesman said at the time: “The fire brigade have dealt with the incident between Chester and Crewe and trains are now running normally between the stations.”