"I wish I hadn't met with him," Gates told Axios on Monday.
Epstein arranged at least $7.5 million in donations to the Massachusetts Institute of Technology (MIT) in 2014, which included $2 million from Gates and $5.5 million from investor Leon Black, according to emails obtained by The New Yorker.
"I won't say I knew him that well, because he was introduced to me as somebody who could bring more people into philanthropy," Gates said. "There were meetings along those lines. That didn't materialize, and so then I stopped meeting with him."
"I'd say I didn't have a ... business or personal relationship -- I wouldn't go that far," he stated.
Gates gave $2 million to MIT's Media Lab, then under the direction of Joichi Ito, for "continued research," according to 2014 letter obtained by Axios.
"Please note that Bill wishes to remain anonymous with this contribution," Gates' agent said in the letter.
Prior to the donation, Epstein had reportedly emailed Ito and said Gates wanted "a write-up on our one science program," per Axios. Gates made his donation less than a month later.
The school took about $800,000 from Epstein over 20 years, MIT President L. Rafael Reif has said.
"[T]he acceptance of the Epstein gifts involved a mistake of judgment," Reif said. "We are actively assessing how best to improve our policies, processes and procedures to fully reflect MIT’s values and prevent such mistakes in the future. Our internal review process continues, and what we learn from it will inform the path ahead."
Harvard University on Thursday disclosed that it received nearly $9 million in donations from Epstein over a nine-year period.
Epstein gave $6.5 million to the Ivy League university's Program for Evolutionary Dynamics and made other gifts totaling $2.4 million between 1998 and 2007, University President Lawrence S. Bacow said.
"Each of these gifts from Epstein and his affiliated foundations to Harvard University predates his guilty plea in June 2008," Bacow said in an email. "To date, we have uncovered no gifts received from Epstein or his foundation following his guilty plea. Moreover, we specifically rejected a gift from Epstein following his conviction in 2008."
Epstein, who was found hanging in his prison cell and later declared dead Aug. 10, had pleaded guilty to a child prostitution charge in 2008 and registered as a sex offender. He served nearly 13 months in jail with work-release privileges after agreeing to a plea deal. Epstein, 66, was awaiting trial on federal sex trafficking charges when he died. His death was ruled a suicide.
Fox News' Vandana Rambaran contributed to this report.