"Two martyrs were recovered and 15 injured, including 10 children" after Israeli planes struck the Salah al-Din school in Gaza City, agency spokesman Mahmud Bassal told AFP.
The Israeli military said in a statement that the air force "conducted a precise strike on Hamas terrorists who were operating inside a command and control centre" located in the school compound.
"Hamas operatives used the compound as a hideout and a base to plan and execute attacks against IDF (Israel Defense Forces) troops and the State of Israel," a statement said.
In recent weeks, the Israeli military has struck several schools across Gaza, primarily in Gaza City, saying they housed Hamas command centres, which the militant group denies.
On Tuesday, Bassal told AFP that a strike on the Mustafa Hafiz school in the city killed at least 12 people.
And earlier this month Israel struck the Al-Tabieen school, also in Gaza City, an attack the civil defence agency said killed 93 Palestinians, while the military said 31 militants died.
Tens of thousands of displaced people have taken refuge in schools since the Israel-Hamas war broke out on October 7 after Palestinian militants attacked southern Israel.
That attack resulted in the deaths of 1,199 people, mostly civilians, according to an AFP tally based on Israeli official figures.
Militants also seized 251 people, 105 of whom are still held captive in Gaza, including 34 the military says are dead.
Israel's retaliatory military offensive against Hamas has killed at least 40,223 people in Gaza, according to the Hamas-run territory's health ministry, which does not give a breakdown of civilian and militant deaths. Most of the dead in Gaza are women and children, according to the UN human rights office.