A Mpumalanga pupil is set to appear in the Kanyamazane Periodical Court on Friday for allegedly raping and murdering another school pupil who vanished after a study session.

The 17-year-old also faces a charge of defeating the ends of justice after he allegedly buried his victim.

"The incident occurred at Ncakeni, Pienaar, near Nelspruit" on April 8, said police spokesperson Brig Leonard Hlathi. "It is alleged that the victim, a 16-year-old girl, left home for a study session but never returned home.

"The following day, her parents searched for her in the area, with no success. They, however, learnt that she was last seen with the suspect, after the study session on that day," said Hlathi.

"Police immediately confronted the suspect and enquired about the whereabouts of the victim. He initially claimed that she had driven off with an unknown man, whom he thought was her uncle," said Hlathi.

"As the interrogation intensified he changed his tune and said the victim had died as a result of strangulation and he buried her out of fear of being arrested."

The teen pointed out the burial spot - a shallow grave in Pienaar - to the police.

Hlathi said the postmortem report revealed that she may have also been raped before she was murdered.

"Police have in the meantime taken in a second person for questioning," said Hlathi.