The Israeli military said it was looking into the reported attack, the second to hit a school in less than a week.
Most Israeli troops are believed to have now pulled out of Gaza. An Israeli military spokesman stopped short of calling the move a withdrawal, but said residents from a number of evacuated Palestinian neighbourhoods had been told they could return.
In the town of Rafah, where the military has been battling militants, a missile from an Israeli aircraft struck the entrance to the school, where Palestinians who had fled their homes were sheltering.
Last Wednesday, at least 15 Palestinians who sought refuge in a UN-run school in Jabalya refugee camp were killed during fighting
Earlier on Sunday, Israeli shelling killed at least 30 people in Gaza, a day after Prime Minister Benjamin Netanyahu vowed to keep up pressure on Hamas.
In Cairo, efforts to find a new truce were resuming. A delegation from Palestinian militant groups Hamas and Islamic Jihad arrived in the Egyptian capital, but a quick breakthrough seemed unlikely in the absence of Israeli representatives.
In Gaza, Israel intensified attacks in the area of Rafah along the border with Egypt, where officer Hadar Goldin, 23, was feared captured on Friday shortly after what was to have been a 72-hour truce began.
The military later said the soldier had died in action.