The teacher was denied bail during his appearance on Wednesday and the matter was postponed to December 10, NPA spokeswoman Phindi Louw said.
The 10-year-old and another boy allegedly damaged a textbook on November 20 and the teacher told them to stay behind after school as punishment, Captain Mponde Khoza said at the time.
The teacher ordered the boys to lie on the classroom floor, then let one boy go.
“He then ordered the remaining boy to take his pants off while the teacher was sitting half-naked on a chair,” Khoza said.
The teacher then allegedly raped the 10-year-old boy and let him go home. He was arrested on November 21 after the boy reported the crime to his mother.