Smoke was spotted coming from the rear of the nine-carriage service when it pulled into the station shortly before 11pm.
Train staff began tackling the incident using fire extinguishers before firefighters arrived and completed the job.
An engineer was called and, after checks were carried out, the train was given the all-clear to continue its journey to Leeds at about 12.30am.
Around 150 passengers are estimated to have been on the service when it got into Wakefield.
No one was injured in the incident, said a spokesman for West Yorkshire Fire and Rescue Service.
Trains were stopped in both directions either side of the station while the fire was dealt with.
Overhead line equipment was also temporarily isolated.
Fire crews from Wakefield, Ossett and Normanton attended the scene.