The schools are run by the UN agency for Palestinian refugees, UNRWA, which Israel has banned from operating on its soil.
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Palestinian students at six UN-run schools in east Jerusalem were forced to leave early on Thursday after Israeli forces permanently shut them down.
Israel's Education Ministry ordered the schools' closure last month, giving them 30 days to shut down, which ended on Wednesday.
The schools are operated by the UN agency for Palestinian refugees, UNRWA, which Israel banned from operating on its soil earlier this year. The organisation continues to run schools in the Israeli-occupied West Bank.
The UNRWA ban was the culmination of a long campaign against the agency, which intensified after the 7 October 2023 Hamas attacks on Israel that ignited the war in Gaza.
Israel claims UNRWA is infiltrated by the Palestinian militant group, and that the organisation teaches antisemitic content and anti-Israel sentiment. UNRWA denies the allegations.
UNRWA is the main provider of education and health care to Palestinian refugees across east Jerusalem, which Israel captured in the 1967 Six-Day War. Israel has annexed east Jerusalem and considers the entire city its unified capital, but the claim is not recognised by most of the international community.
The Israeli Ministry of Education says it will place the students into other Jerusalem schools, but parents, teachers and administrators warn that closing the main schools in east Jerusalem will force their children to cross crowded and dangerous checkpoints every day. Some do not have the correct permits to pass through.
Some 800 Palestinian students are at risk of missing out on their education altogether if they cannot be placed in different schools.
The Ministry of Education said it was closing the schools because they were operating without a license. UNRWA administrators pledged to keep the schools open for as long as possible.