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 coaches of the passenger train.
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.
Media reports quoted officials as saying that "human remains" have been found from the blast site, leading to believe that a suicide bomber attacked the train.