Mnookin will assume her new post on 1 July, becoming the university's fifth leader in the past four years, following a period of significant campus turmoil.
The university experienced unrest due to campus protests over the Israel-Hamas war and a campaign by the Trump administration to influence student activism.
This campaign included the cancellation of $400 million in research grants and pressure to adopt a contentious, federally endorsed definition of antisemitism.
Columbia ultimately reached a settlement, paying over $220 million to restore research funds and agreeing to overhaul its student disciplinary process.