Sarah's Trust will close "for the foreseeable future" after "some months" of discussion, a spokesman said.
More than three million documents were published by the US Department of Justice on Friday relating to Epstein, revealing more about his contact with the former prince Andrew and his ex-wife.
A spokesman for Sarah's Trust confirmed the closure on Monday.
"Our chair Sarah Ferguson and the board of trustees have agreed that with regret the charity will shortly close for the foreseeable future," he said.
"This has been under discussion and in train for some months.
"We remain extremely proud of the work of the trust over recent years.
"We have partnered with over 60 other charities in over 20 countries, providing education, healthcare, crisis response and environmental projects," he said.
"We delivered over 150,000 aid parcels during the Covid pandemic, provided medical aid and training for those affected by the war in Ukraine and delivered education for over 200 children in Ghana."
In the document dump, Ferguson accuses Epstein of using her.
It's "crystal clear to me that you were only friends with me to get to Andrew", she wrote.
In an email exchange from September 21, 2011, she congratulated him on the birth of a baby.
"Don't know if you are still on this bbm but heard from The Duke that you have had a baby boy," she wrote.
"Even though you never kept in touch, I still am here with love, friendship and congratualtions (sic) on your baby boy. Sarah xx"
The email is then followed up with a message saying: "You have disappeared".
"I did not even know you were having a baby. It was soooo crystal clear to me that you were only friends with me to get to Andrew. And that really hurt me deeeply (sic). More than you will know."
Other emails also revealed that in August 2009, "Sarah" thanked Epstein for "being the brother I have always wished for" and she has "never been more touched by a friends kindness".
In April 2009, "Sarah" emailed Epstein calling him "my dear spectacular and special friend Jeffrey" and a "legend", adding that she was "so proud" of him.
The exchanges are all dated after Epstein was convicted in 2008 for prostituting minors.
Elsewhere in the document dump, screenshots and scans appear to show Mountbatten-Windsor exchanged emails with Epstein about a "beautiful" Russian woman, and invited him to Buckingham Palace.
The former Duke of York was stripped of his titles by the King last year after the posthumous publication of a book by Virginia Giuffre, saying she was trafficked by Epstein and his former girlfriend Ghislaine Maxwell when she was 17.
Mountbatten-Windsor paid millions to Giuffre, a woman he has claimed never to have met, to settle a civil sexual assault claim in 2022.
The former prince has vehemently denied any wrongdoing.
