The university was at the forefront of US campus protests last spring against Israel's war on Gaza. Pro-Palestinian activists set up an encampment in April and inspired a wave of similar protests.
The move came a day after Trump signed an executive order saying that Washington would withdraw from a number of UN bodies, including the Rights Council.
Explaining why Harris skipped Israeli Prime Minister Netanyahu's speech at the US Congress to honour a prior commitment, Trump accused her of anti-Semitism.
"We see prominent academic institutions, halls of history, culture, and education contaminated by hatred and anti-Semitism fuelled by arrogance and ignorance," he said.
