"Palestine Red Crescent teams responded to 28 fatalities and 54 injuries following the Israeli occupation army's targeting of Rafida School," the organisation said, referring to a school in Deir el-Balah.
Gaza's Hamas-run health ministry issued the same death toll in a statement.
The Israeli army said in a statement the strike targeted Palestinian combatants operating from a command-and-control centre "embedded inside a compound that previously served as the (Rafida) School".
It did not give a toll but said the command-and-control centre was used "to plan and execute terrorist attacks against IDF (army) troops and the State of Israel".
Thursday's attack was the latest in a series of Israeli strikes on school buildings housing displaced Palestinians in Gaza, where fighting has raged for more than a year.
On September 26, at least 15 people were killed in another school-turned-shelter strike in northern Gaza's Jabalia camp, according to Gaza civil defence agency.
The Israeli military is currently engaged in an intense operation in Jabalia.
The Israeli military accuses Hamas of hiding in school buildings where thousands of Gazans have sought shelter -- a charge denied by the Palestinian militant group.
On Thursday evening, the Israeli army announced in a separate statement it had struck a medical compound in the northern Gaza city of Jabalia the previous day, killing at least 12 fighters from Palestinian Islamist movement Hamas and Palestinian Islamic Jihad.
Without naming it, the military said the "area that previously served as a medical compound in Jabalia" was used as a "command and control centre" where large quantities of weapons were stored.
The military said among those killed were also some who took part in carrying out the October 7, 2023 attack on Israel.
A local source from Jabalia who wished to remain anonymous for safety reasons told AFP Thursday that Israeli aircraft struck the city's Al-Yemen Al-Saeed Hospital, where displaced Gazans had sought refuge.
The source said that "among the martyrs pulled from the rubble of two destroyed rooms were dismembered bodies, cases of amputations, and burned corpses".
A witness who also did not want to be named said among the corpses were people who belonged to Hamas and Islamic Jihad.
Ongoing Israeli military operations in Jabalia have killed at least 140 people over the past six days, according to Gaza's civil defence agency.
At least 42,065 Palestinians, a majority of them civilians, have been killed in Israel's military campaign in Gaza since the war began, according to data provided by the health ministry in the Hamas-run territory.
The United Nations has acknowledged the figures to be reliable.
The October 7 attack that triggered the war resulted in the deaths of 1,206 people on the Israeli side, most of them civilians, according to an AFP tally based on official Israeli figures, which includes hostages killed in captivity.
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