Principal Jolanie Roos told the HERAUT the lone burglar, who was captured on camera footage, broke into classrooms by breaking a window and damaged a toy till to search for money.
Stolen items include an external hard drive, a computer, a TV, electrical equipment and educational software for the children.
The intruder even helped himself to some yoghurt.
After he was finished in the classrooms, he went to Zoë Skool, where he further wreaked havoc.
A first-aid kit and an electrical fan were found abandoned on the property.
The specialised schools cater for children with different needs.
“When something like this occurs it sets us back tremendously,” said Roos.
A case was opened at the SAPS.
Anyone with information regarding the incident is urged to contact the police.