One soldier also died in the shootout in the Mir Ali area of the North Waziristan District, the military said.
The region had been a safe haven for militants for decades until the Pakistani military carried out a major operation following an attack on an army-run school in Peshawar in 2014.
This terrorist attack killed more than 150 people, mostly school children.
The army had announced it had cleared the region of local and foreign militants after a yearlong operation.
But occasional attacks have continued, raising concerns that the local Taliban, who found sanctuaries in Afghanistan, are regrouping in the area, according to the Associated Press.
The Pakistani Taliban, also known as Tehreek-e-Taliban Pakistan, or TTP, are separate from, but allied with, the Afghan Taliban, who seized power last year as US and NATO troops pulled out from Afghanistan after 20 years of war.
The two have overlapping ideologies of establishing a strict Sharia system and opposing Americans.
TTP reportedly has several thousand fighters on both sides of the Afghanistan-Pakistan border.
It was set up in 2007 when many outlawed groups in Pakistan banded together to fight the federal government.
The Pakistani army launched a massive operation to crack down on the group in 2014 following a TTP attack on the Karachi airport that killed 36 people, and another attack on the Peshawar Army Public School that killed 130 children.
TTP was largely considered suppressed after the operation, with the Pakistani army claiming it killed thousands of militants and forced others to flee the border, however, occassional attacks also occur in northwest parts of the country.