The stoning was supposedly carried out Monday in the Khwezai-Baezai tribal area, Dawn newspaper reported. The area is part of the Federally Administered Tribal Areas along Pakistan's border with Afghanistan.
It was first such reported incident of a stoning by the militants, who usually put the accused before firing squads, the report said.
A spokesman for the militants claimed the woman, who was married and living in Peshawar, had eloped with the accused man last month. The spokesman alleged a complaint was received from the woman's family that she had been abducted but it was later found by Taliban members who captured the couple that she had eloped with the man.
The spokesman said the tribal court found them guilty of adultery and sentenced them to death by stoning, the Dawn report said.
The woman's body was buried in the area while the man's body was given to his relatives.