The boy had been missing since Saturday and his body was found in a pond on the outskirts of Dera Murad Jamali town yesterday.
Police said some people kidnapped the boy and killed him after sexually abusing him, a media reported.
Police surgeon Dr Ibrahim Kandrani confirmed that the boy had been sexually abused. He said that wounds inflicted by a dagger-like object were found on the boy's forehead and mouth.
Fingerprints were also visible on his neck which showed that he had been strangled. Police have registered a case and taken three people into custody for interrogation.
Cases of violence against children are on the rise in conservative Pakistan despite efforts to improve security of children and other vulnerable groups.