North Yorkshire Fire & Rescue Service said crews were called out to the stricken service just south of York station, near the city’s racecourse.
A spokesman said 54 passengers and four staff were helped from the train, on to a replacement service.
He said: “When crews arrived, they confirmed a fire had occurred on an express passenger train.
“The fire was in the rear engine. It was extinguished by the train’s own fire prevention system.”
He added: “However, the decision was made to assist with the evacuation of 54 passengers and four staff on to a second train and transport them back to York rail station.
“Fire and rescue crews cooled the rear engine using two foam extensions and checked for residual heat with a thermal image camera.”
There were delays to some services in and out of York this morning.
Separately, there were major delays and cancellations on services between Ilkley, Leeds and Bradford this morning. Network rail blamed a “train fault”.
Passengers on one train were forced to wait 40 minutes between stops.