The foundation has been mired in controversy due to chairman Bill Gates' association with Epstein.
A release of emails in January by the US Justice Department also showed communication between Epstein and the Gates Foundation's staff.
"Early this year, Gates Foundation CEO Mark Suzman commissioned an external review to assess past foundation engagement with Epstein, and our current policies for vetting and developing new philanthropic partnerships," the foundation said in a statement on Tuesday.
"That review is under way, and we expect the board and management will receive an update this summer."
The Wall Street Journal, which first reported the news earlier on Tuesday, said Suzman told staff in a memo, "This is a challenging time for our organisation in many ways, but it also highlights the critical importance of taking the tough actions now".
The foundation told Reuters the review was announced in an organisation-wide email in March.
It said in February that it did not make any financial payments to Epstein or employ him at any time and that it regrets having any employees interact with him in any way.
The DOJ documents also included photos of Bill Gates posing with Epstein, as well as with women whose faces were redacted.
Gates has said his relationship with Epstein was confined to philanthropy, and that it was a mistake to meet with him. He has also denied spending time with victims of the financier's sexual abuse.
A spokesperson for the organisation told Reuters that during a town hall meeting with foundation employees in February, Gates "took responsibility for his actions" regarding his ties to Epstein.
Bill Gates is the chair and a board member of the foundation started by him and his then-wife in 2000, which is one of the world's biggest funders of global health initiatives.
