The foundation and the auction house announced the agreement on Wednesday.
The foundation said the money raised for its endowment from the sales would allow it to expand support of the visual arts, fulfilling Warhol's purpose in establishing it.
The agreement will mean Christie's will hold a series of sales over the coming years, including auctions, private sales and online events.
The foundation said it would also made donations to museums.
The collection includes items ranging from prints to photographs, some of which have been seen by the public.