The 18-year-old boy allegedly broke into the school in September.
He was arrested on Tuesday and released on bail.
On Wednesday, he appeared in the Kempton Park Magistrate's Court on a burglary charge.
A charge of crimen injuria in connection with the nude images was added to the burglary charge.
It was not known if anything was stolen during the break-in at the school.
Magistrate Prince Manyathi postponed the case to next month for further investigation.
The pupil's lawyer Andre Swanepoel told the paper that his client would continue with his matric exams.