A Sapa correspondent reported the man, 29, from Langeloop village near both the Swaziland and Mozambique borders, was not asked to plead.
He allegedly raped his son during school holidays in June.
According to police, the boy and his eight-year-old brother live with their mother at Sikhwahlane village, also near the Swaziland border.
Lieutenant Mzwandile Nyambi said: “They went to visit their father for the school holidays. Their mother learnt about the abuse of the four-year-old after the eight-year-old disclosed the matter to their aunt.”
He said the boy was taken to hospital where it was confirmed he had been raped.
Magistrate Hazel Khoza postponed the case to October 6 for further investigation.