Gauteng police say the young girl had been raped and murdered.
A 44-year-old man has been arrested in connection with her death.
"The suspect has been sought by the police after he raped and murdered a 12-year-old girl in Refilwe, Cullinan, on Monday 22 May," says police spokesperson Kay Makhubele.
He says the child had gone looking for her mother at her boyfriend's home.
The suspect is expected to appear in the Cullinan Magistrate's Court soon, facing charges of rape and murder.