The Jaffer Express was hit by the remote-controlled bomb near Bakhtiarabad area of Sibi in the Balochistan province while coming from Rawalpindi to Quetta.
A police official said that one passenger was killed and five others injured in the attack.
"It was an improvised explosive device which was planted on a track some 150 kilometres from Quetta," Balochistan Home Minister Mir Sarfaraz Bugti said.
He said a three feet section of the track was destroyed in the blast which left one passenger dead and five others wounded. The injured were shifted to hospital for treatment.
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Paramilitary forces and police arrived at the scene and launched search operation. No groups claimed responsibility.
Balochistan Chief Minister Sanaullah Khan Zehri condemned today's attack and sought an inquiry report.
Attacks on trains are common in Balochistan where Baloch nationalists are fighting for greater control over natural resources.
This is not the first time that the Jaffar Express has come under attack. Four people were killed in November last year when the Rawalpindi-bound train was attacked with bomb planted on its track in Mastung.