The train, which departed from Rawalpindi, was passing through Dera Murad Jamali district of the restive Balochistan province when the blast occurred causing damage to at least four bogies of the passenger train.
Media reports had earlier suggested that it was a suicide attack but state-run Radio Pakistan said it was a remote control bomb blast.
Emergency and rescue team were dispatched to the site.
Security personnel reached the site and cordoned off the area as a probe into the incident went underway.