Police spokesperson Brigadier Sabata Mokgwabone said the body was discovered on Sunday, at Extension 7, in the bushes.
"The minor was last seen on Friday, [12 May 2017] when her grandmother sent her to one of the neighbours. She did not come back home and a missing person case was eventually reported to the police on Saturday."
He said following an intensive investigation, 32-year-old man was arrested on Sunday evening at Extension 7, Jouberton.
He was expected to appear in the Klerksdorp Magistrate's Court on Tuesday, facing a charge of murder.