The province's homeland secretary, Asad Gilani, said militants targeted the train in the Notal area of Naseerabad district, Dawn News reported.
"When the train reached Notal, there were huge explosions," Gilani said.
The bomb damaged a portion of the tracks and part of the train's undercarriage. Sources told GEO TV News the bomb was so powerful it left a crater and blew off 5 to 6 feet of track.
Hundreds of passengers from Punjab province were returning to Balochistan on the train after Eid holidays, Dawn News said.
Quetta Superintendent of Railway Police Riaz Ahmed said the bomb was planted on the track and was detonated when the train reached Notal.
Railway traffic between Balochistan and other parts of Pakistan was suspended until the track was repaired and passed a security clearance, Dawn News said.
Police officials said they suspected Baloch rebels placed the bomb but but no one had claimed responsibility for the attack.