A concerned neighbour called police after seeing a group of boys walking on the roof around 8.30pm.
Police arrived just after the boy fell through the skylight.
Detective Sergeant Grayson Joines told the Herald it appeared the boy had sat down on the bubble-like skylight and it had given way.
"The poor little fellow has fallen about 25 feet [7.6m]," he said.
"He fell on to a pretty hard concrete floor with carpet."The boy's friends broke into the classroom the boy landed in to help him.
"The two boys were dragging their friend, who was near unconscious, out of the building," Joines said.
The officers gave first aid to the boy until an ambulance arrived.Central Normal School principal Shona Oliver could not comment on the incident as police were investigating.
She did not know the identity of the injured boy or whether he was one ofthe school's pupils.
Police have spoken to the injured boy's friends and will contact the 12-year-old and his family when he is in a better condition.
His family are with him in hospital and are being supported by the police and Victim Support.
Police said the start of the school holidays was a timely reminder for parents to talk to their children about staying safe and not to take any unnecessary risks.