She said she made the announcement now so new leadership could be in place before the new term begins on Sept. 3, when student protesters have vowed to resume protests.
The university announced Katrina Armstrong, dean of Columbia's medical school, would serve as interim president.
Students with Columbia University Apartheid Divest, a group behind the protests, welcomed the resignation but said it should not become a distraction from their efforts to have Columbia divest from companies that support Israel's military and its occupation of Palestinian territories.
"We hope that Columbia will finally appoint a president that will hear the students and faculty rather than appeasing Congress and donors," said Mahmoud Khalil, one of the group's lead negotiators with the school's administration.
Israel waged its brutal war on besieged Gaza on October 7 after Hamas carried out an unprecedented operation against the occupying entity in retaliation for its intensified atrocities against the Palestinian people.
Israel has imposed a complete siege on the densely populated territory, cutting off fuel, electricity, food, and water to the more than two million Palestinians living there.