US media outlets have unearthed several instances of alleged plagiarism in her academic record. Harvard's board investigated the allegations last month, and found two published papers that required additional citation.
Harvard University's president has resigned after facing allegations of plagiarism and criticism over her comments about antisemitism on campus.
Claudine Gay had faced mounting pressure to step down in recent weeks.
In a letter announcing her resignation, she said it was in the "best interests" of the university for her to step down.
"It has been distressing to have doubt cast on my commitments to confronting hate and to upholding scholarly rigour," she said.
"This is not a decision I came to easily. Indeed, it has been difficult beyond words," Dr Gay wrote, adding that her resignation would allow Harvard to "focus on the institution rather than any individual."
She said she had been subjected to personal threats and "racial animus".
The 53-year-old served as president for six months and was the first black person, and only the second woman, to be appointed to lead the Ivy League university. Her tenure was the shortest in its 388-year history.
Harvard is one of several universities in the US accused of failing to protect its Jewish students following the outbreak of the Israel-Hamas war in October. Jewish groups have reported an alarming rise in antisemitic incidents in the US since the conflict began.
During a tense congressional hearing last month, Dr Gay said calls for the killing of Jews were abhorrent. She added, however, that it would depend on the context whether such comments would constitute a violation of Harvard's code of conduct regarding bullying and harassment.
That comment prompted a widespread backlash and she later apologised in an interview with the university's student newspaper. "When words amplify distress and pain, I don't know how you could feel anything but regret," Dr Gay said.