The pupil, aged 16, was taken to Aberdeen Royal Infirmary, but police later confirmed that he had died.
Another pupil, believed to be around 16-years-old, has been detained by police.
Officers are still currently surrounding the school.
Speaking earlier today, Chief Inspector Graeme Mackie said: “This is a shocking and extraordinary incident for Aberdeen and firstly our thoughts are with the family and friends of the boy who has sadly lost his life today.
“A full and thorough inquiry is under way has been launched and there will be a police presence in the area for the foreseeable future.
“We are working closely with the education authorities and wider community as I am sure this incident will be felt not only in Aberdeen but much further afield.”
A spokesman for Aberdeen City Council confirmed this afternoon that the school will be closed tomorrow.
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