The fire broke out at the old Westercommon Primary, in the East End, which has been reduced to a charred shell.
Huge flames could be seen billowing from the building in Ellesmere Street.
This morning, blackened walls were visible and the roof had been destroyed almost.
Fire crews were called to the scene shortly before 3am.
A Strathclyde Fire and Rescue spokesman said about a third of the school had been affected.
Group Commander Eddie Mullen said: "The crews were faced with a well developed fire from the outset and they worked tirelessly in difficult conditions to prevent the spread of fire to other parts of the building and neighbouring properties."
A joint investigation, between Strathclyde Fire and Rescue and Strathclyde Police, will get under way today to find the cause of the blaze.
The building has been lying empty since May 2012.
Pupils transferred to a new site at Benview Campus in Ruchill.
The site is owned by City Property, an arm's length organisation of Glasgow City Council.
Roads around the school were closed today and diversions were put in place to allow emergency services to deal with the fire.