The report by the UN Independent International Commission of Inquiry on the Occupied Palestinian Territory, including East Jerusalem, and Israel examined violations against Palestinian children since the start of the war between Israel and Hamas on October 7, 2023.
Around 30 per cent of those killed in the Gaza war were children, the report found.
A previous report by the commission in September found Israel had committed genocide in Gaza and that top Israeli officials including Prime Minister Benjamin Netanyahu incited these acts - accusations that Israel called scandalous.
Israel's mission in Geneva said Israel rejected what it called the Commission's "second defamatory advocacy report".
"Israel dismisses this libelous sham," it said in a statement, adding "every child deserves protection" and asserting that the report ignored "the brutal tactics of Hamas".
The UN commission said Palestinian children were deliberately targeted and killed during the war, including after a ceasefire came into effect in October 2025. It said this was a key element establishing genocidal intent by Israeli authorities and security forces to destroy the Palestinian group, in whole or in part, in Gaza.
"The evidence shows that Palestinian children have been deliberately targeted and killed by the Israeli security forces," said Srinivasan Muralidhar, the commission's chair, in a statement accompanying the report.
The report found the proportion of children killed was higher than in previous conflicts. Between October 7, 2023 and October 7, 2025, at least 20,179 children were killed, around 30 per cent of the overall death toll.
By comparison, in hostilities in Gaza in 2008-2009 and 2014, children made up approximately 24 per cent of conflict-related fatalities, the report said.
Israeli forces continued to use high-payload munitions and weapons with wide-area effects in densely populated residential areas despite mounting child casualties, the commission said.
"This indicates that such attacks, which killed children in such high numbers, were intentional," it said.
The commission said it believed children were targeted collectively because the Israeli security forces considered the civilian population as a whole to be associated with Hamas and other armed groups.
A rebuttal shared by Israel's mission in Geneva said Israel "consistently strives to minimise harm to children even in situations of conflict" and that Israel rejected the suggestion it deliberately targets children "in the strongest terms".
Muralidhar said by targeting children, Israel was undermining the capacity of the Palestinian people to exist and to determine their future.
Conditions imposed by Israel in Gaza, including widespread attacks, repeated displacement and starvation caused by the blockade of aid, food and medicine, severely harmed children's health and development, resulting in preventable deaths and trauma, the report said.
Israel's rebuttal said the report failed to mention Israel's role in facilitating vaccinations and the entry of medical staff, and the establishment of field hospitals. It accused Hamas of systematically diverting humanitarian aid and fuel for hospitals. Hamas has rejected such accusations.
In the West Bank, including East Jerusalem, the Commission found a sharp increase in violence by Israeli settlers against Palestinian children and documented evidence of torture, including sexual and gender-based violence, during mass arrests and detention.
It said Palestinian children, particularly boys, were subjected to systematic mistreatment in detention, including forced stripping, beatings and food deprivation.
The commission concluded the treatment constituted the crimes against humanity of torture and other inhumane acts causing great suffering or serious injury.
Israel's rebuttal said the report's findings on the West Bank omitted context on the "constant terrorist threat" that it said Israeli security forces were responding to.
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