The bomb was planted on a road in Nasti Kot area of Kurram tribal district and hit the van as it drove the children to the school.
A security official said the driver of the vehicle and the boy were killed, while five more children were injured.
Nobody took responsibility of the attack but the Taliban militants are active in the region and often target the security forces and civilians.
Kurram on Afghan border is one of seven tribal areas controlled through colonial era draconian laws.