About 120 patients, including premature babies, had to stay behind and were being cared for by a skeleton staff.
Those who left, including the sick and injured, walked through rubble-strewn streets – but it is unclear where they will go as more than half of Gaza’s 35 hospitals are no longer operational.
Journalist Khader Al Zaanoun said: “We raised our hands and carried white flags.
“Last night was very difficult. The sounds of explosions and gunfire were terrifying.
Philippe Lazzarini, the commissioner general of the UN’s aid agency in Palestine, said: “These attacks cannot be commonplace, they must stop.
“A humanitarian ceasefire cannot wait any longer.”
Catherine Russell, of Unicef, said: “We’re seeing horrifying images of children and civilians killed in Gaza – yet again – as they shelter in a school, which must always be protected.”
Israeli authorities yesterday urged people in Khan Yunis, the largest city in southern Gaza – where whole streets have already been destroyed in airstrikes – to evacuate by late afternoon.
Meanwhile, the first flight carrying 15 injured children and their families from Gaza arrived in the UAE yesterday. They entered Egypt via the Rafah Crossing, before boarding a flight to Abu Dhabi.
Amr Jandieh, 12, travelled alone after his father and uncle were killed right in front of him as they chatted in the street.
He recalled: “All of a sudden a missile hit and I lost consciousness. I woke up and found myself in the hospital.”
The UAE plans to bring around 1,000 children from Gaza for hospital treatment over the next few weeks, while the Emirati branch of the Red Crescent is building a field hospital on the Egyptian side of the crossing.
And more than 30,000 people ended their march from Tel Aviv to Jerusalem by holding a rally outside the offices of the Prime Minister Benjamin Netanyahu, pressuring him to secure the 240 Israeli hostages’ release. Foreign Secretary Lord Cameron spoke to his Israeli counterpart on Friday to emphasise “the need for humanitarian pauses”, to prevent “wider regional instability”.