Two coaches of the Khushal Express derailed after the explosion near Thul town of Jacobabad district at 2 am, police officials said.
The train was going from Karachi, the capital of Sindh, to the northwestern city of Peshawar.
Police said there would have been more casualties if the coaches had overturned.
The injured were taken to a nearby hospital.
No group claimed responsibility for the attack.
In the past, some hitherto unheard of groups from Sindh have claimed responsibility for bomb attacks on railway tracks in the province.