A tribal council in the town of Parachinar, close to the Afghan border in Kurram district, ordered the sentence on Anwar-ud Din, who was about 25 years old, for having “illicit relations” with a local girl.
“There were some 40 to 50 people who hit the man with stones till he bled to death,” a local tribesman told AFP on condition of anonymity.
Relations between men and women without family approval are considered immoral by many in Pakistan, particularly in the deeply conservative northwestern tribal areas, where Taliban and Al Qaeda linked militants have strongholds.
Hundreds are killed around the country each year in the name of defending family “honour”, but stonings are extremely rare.
Din was accused of having an affair with an 18-year-old girl and meeting her secretly, but both were caught on Sunday in a graveyard, the tribesman told AFP.
The soldier admitted he had met the girl three or more times before and the punishment was carried out on Tuesday in the graveyard where the pair were discovered, the tribesman said, adding that the body was later taken to hospital.
Local government and security officials confirmed the incident, but declined to comment.
The fate of the girl remains unclear, but there were rumours in the area that she may also have been executed, although she denied the affair, the tribesman said.
A hospital official confirmed that they had received a mutilated body on Tuesday, which was later taken away by paramilitary forces.
“It was really a horrific sight. The body had been badly damaged after being hit by stones. Wounds all over and the face could no longer be recognised,” the official said.
Pakistan’s seven tribal districts bordering Afghanistan do not have a regular legal system and justice is dispensed according to tribal and Islamic custom by councils of elders.