"After giving the matter a great deal of thought over the past several days and weeks, I think that it is best that I resign as director of the media lab and as a professor and employee of the Institute, effective immediately," he wrote in an email to the university's provost and shared with The Times.
Administrators of the MIT lab had reportedly tried to hide a relationship with Epstein, the disgraced financier who killed himself in jail last month while facing federal sex trafficking charges.
MIT has said that it received $800,000 from Epstein over the span of 20 years, and apologized for accepting those contributions. Ito said this past week that he had taken $525,000 of Epstein's money for the lab and $1.2 million for investment funds he controlled separately.
But documents obtained by The New Yorker showed that the lab had been aware of Epstein's status as a convicted sex offender and continuing to accept money from him, marking his contributions as anonymous.
Epstein had solicited millions of dollars in donations from individuals and organizations, including Microsoft founder Bill Gates and investor Leon Black, according to The New Yorker. He secured at least $7.5 million in donations for the lab, including $2 million dollars from Gates and $5.5 million from Black, the magazine reported.
A Gates spokesperson said on Saturday that Epstein was introduced to Gates "as someone who was interested in helping grow philanthropy" but that "any claim that Epstein directed any programmatic or personal grantmaking for Bill Gates is completely false."
A spokesperson for Black declined to comment.
- CNBC's Brian Schwartz contributed reporting