The attack occurred on Saturday in a village close to Miran Shah, the main town in North Waziristan.
Pakistan has deployed thousands of troops and security forces in the mainly tribal region in effort to flush out suspected members of the Taliban, al-Qaida and their local supporters.
A senior security official, speaking on condition of anonymity, said all eight soldiers guarding the checkpoint were killed.
Another security official, again remaining anonymous, said that the dead troops had moved to the new checkpoint only hours before the attack.
He said Pakistani forces supported by helicopters were trying to track down the assailants.
The checkpoint was built as part of Pakistan's efforts to stop potential terrorists travelling unmonitored between Pakistan and Afghanistan, where US forces are trying to combat rebels.
Pakistan is a key ally of the United States in its war on terror and it has killed or captured scores of supspected terrorists in Waziristan regions since the 9/11 attacks.