A military statement said the suicide bomber triggered his explosives-laden vest near a vehicle on security patrol in a village near the town of Mir Ali in the tribal district of North Waziristan.
The attack killed two soldiers in the vehicle on the spot and wounded another. Three children playing alongside the road were critically wounded. All of the wounded were rushed to a hospital in a helicopter but none survived, the statement said.
The attackers made no immediate claim of responsibility. Security officers and intelligence officials were investigating the area for the bomber's handlers, according to the military.
Three children ages four to eleven years old, as well as three soldiers, were killed in the heavily militarised area, according to Pakistan's army.
"The bomber came by foot and blew himself up when a vehicle of security forces passed by," a local government official told AFP on condition of anonymity.
Pakistan prime minister Shehbaz Sharif said that "murderers of innocent children are enemies of humanity and Islam".
"We will not sit in peace until we hunt down these barbarians and those who patronise them," he added in a statement.
The attack has not yet been claimed by any militant groups.
The Pakistani Taliban -- Tehreek-e-Taliban Pakistan (TTP) -- has a long history of plotting strikes in the region.
The group is responsible for some of Pakistan's worst incidents in recent history.
Islamabad has become extremely assertive about providing safe haven to militants planning strikes on its side of the border since the Afghan Taliban took back power in Kabul.
However, Saturday's blast came in the midst of a ceasefire to facilitate peace talks.
In a letter, TTP leadership had warned fighters "not to violate the decision taken by the central command".
Separately on Sunday, police said that two Sikh shopkeepers were shot dead by two gunmen riding a motorbike in the northwestern city of Peshawar, 30 kilometres (19 miles) from the Afghan border.
Local police chief Muhammad Ijaz Khan told AFP that "both the men died on the spot and the gunmen escaped from the scene".
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