The man was arrested on Sunday night after he was found with the girl at his house, said Warrant Officer Kay Makhubela.
The girl’s mother reported her missing on Sunday night after she failed to return home from the shop earlier in the day.
Police were told by a local resident that the girl was seen entering a man’s house.
“Police went to the house and broke open the door as the man locked himself and the girl inside,” said Makhubela.
“She was found crying inside the house and was already raped.”
The 23-year-old would appear in the Protea Magistrate’s Court on Tuesday.