The National Audit Office (NAO) said it will scrutinise the financial settlement and deliver a final verdict in March.
It comes after Tory rebel and staunch Remainer Nicky Morgan urged the NAO to consider the “reasonableness of this payment” and assess how the figure was arrived at as Treasury Select Committee chairwoman.
NAO chief Sir Amyas Morse said the watchdog had already begun discussions with the Treasury.
Former Education Secretary Mrs Morgan said: “Various wide-ranging sums for the UK’s withdrawal payment to the EU have been bandied about.
“Last month, the Prime Minister told Parliament that the so-called Brexit divorce bill will be £35 billion-£39 billion.
“Parliament must be able to scrutinise the reasonableness of this bill.
“Accordingly, I have written to Sir Amyas to request that the NAO examines the withdrawal payment, including the assumptions and methodologies used.”
Ms Morgan was one of 11 Tory MPs to vote against the Government in the House of Commons on an amendment that would give MPs the final say on the Brexit deal.
Prime Minister Theresa May told MPs in December Britain would have to stump up between £35 billion and £39 billion to unshackle itself from the EU – as long as a deal on a future trading relationship was agreed.
Sir Amyas said: “I can confirm that we intend to report on the main elements of the financial settlement with the EU.
“We are already in discussions with HM Treasury aimed at planning our work.
“I expect our report to be published in late March.”