The girl lodged a complaint with the police earlier this week.
Police arrested the suspect, who appeared in the Bellville Magistrate's Court on Wednesday. The accused is being held until his next appearance.
A family member told the Cape Times that the girl was living with her mother and had returned to school.
“Her mother brings her to her grandmother's house and collects her and her younger brother in the evenings when she returns from work,” the family member said.
The girl's family insist that no officials have been to counsel her, despite the Department of Social Development saying it had “availed” its trauma debriefing services to the family.
“No officials have been to the grandmother or the mother's home since she reported the case to the police,” a family member said.
Department spokesperson Sihle Ngobese said it had availed its trauma debriefing services to the girl and her family.
Police spokesperson FC van Wyk also said the girl received counselling at the hospital, where she went for her medical assessment.