AFP could not independently verify the toll which, if confirmed, would appear to be one of the largest from a single strike during 10 months of war in Gaza between Israel and Hamas Palestinian militants.
"The death toll is now between 90 to 100 and there are dozens more wounded. Three Israeli rockets hit the school that was housing displaced Palestinians," agency spokesman Mahmud Bassal told AFP.
The government media office in Hamas-ruled Gaza said the strike killed more than 100 people.
With most of Gaza's 2.4 million people displaced during the war started by Hamas's October 7 attack on southern Israel, many have sought refuge in school buildings.
Saturday's incident brings to at least 14 the number of schools struck in Gaza since July 6, killing more than 280 according to an AFP tally of tolls previously given by officials in the territory.
AFPTV live images from the scene showed a large complex with a courtyard where debris lay inside and out. Part of the structure appeared to be a mosque, the upper story of which was partially blown out and charred.
Images showed white-shrouded bodies, blood stains on the ground, and smoke rising from the rubble.
'Precise munitions'
Israel's military said it struck a Hamas "command and control centre" that was "embedded" in Al-Tabieen school in the Daraj neighbourhood.
"Numerous steps were taken to mitigate the risk of harming civilians, including the use of precise munitions, aerial surveillance, and intelligence information," a statement said.
The military has repeatedly made similar accusations after strikes on school shelters. Hamas has previously denied Israeli claims that it uses schools, hospitals and other civilian facilities for military aims.
The Islamic Jihad, a militant group fighting alongside Hamas, said the strike took place "during the dawn prayer".
Ismail al-Thawabta, director general of the Gaza government media office, told AFP that the strike "resulted in more than 100 martyrs and dozens of injuries, most of which are in severe and critical condition".
Gaza government media sources said the school was housing around 250 people, about half of them women and children.
On Thursday, the civil defence agency said Israeli strikes hit two schools in Gaza City, killing more than 18 people. That came after two other schools were hit last Sunday in the city, with at least 30 dead, according to the agency.
The Israeli military said it struck Hamas command centres in both instances.
Israel has vowed to destroy Hamas and in January the military said it had dismantled the group's command structure in northern Gaza. But the military has since found itself returning there and to other areas of the territory to battle militants again.
