Mr Brown will repay the money in full said Downing Street
Prime Minister Gordon Brown will repay £12,415 after an independent audit of all MPs' expenses claims since 2004.
Downing Street confirmed he would repay the money, largely for cleaning and gardening, even though the claims had been within the rules at the time.
It said auditor Sir Thomas Legg had "deemed" that any annual claims above £2,000 for cleaning and £1,000 for gardening should be repaid.
Some MPs are annoyed that new limits are being applied retrospectively.
Conservative leader David Cameron has been asked by Sir Thomas to provide more information about payments for which he over-claimed in 2006 when he changed his mortgage. He had already repaid £218.
Chest of drawers
Lib Dem leader Nick Clegg is to repay £910 of the £3,900 he claimed for gardening between 2006 and 2009.
SNP leader Alex Salmond is repaying £710.88 for removal costs, which he claimed when he gave up his rented flat in London in 2007. He has also been asked to supply more information on £2,610 claimed for hotel stays.
Chancellor Alistair Darling is to repay £554 he claimed towards a chest of drawers to furnish his second home. He claimed £1,104, but Sir Thomas has imposed a limit of £550 for such items.
Meanwhile, shadow chancellor George Osborne has been asked to provide copies of his mortgage interest statements. It is understood that he has not been asked to repay any money.
Sir Thomas, a former civil servant, was asked to scrutinise all MPs' claims after the furore when details were leaked to the Daily Telegraph in May.
THE STORY SO FAR
MPs are allowed to claim expenses for running a second home but there was much uproar in May when receipts and details of what they had been claiming for were leaked to a newspaper.
Among them were claims for expensive TVs and furniture, MPs who claimed for more than one property by "flipping" the designated second home and others who over-claimed for mortgages or services.
Many MPs have announced they will be standing down, some have already repaid claims in response to constituents' anger.
Party leaders pledged to change the system and an independent review is due to make its recommendations this month.
The PM also asked an independent auditor to go over past claims again, to ensure money had been paid out properly.
Some MPs will be told their expenses presented no issues. Others will be asked for more information and many are expected to be asked to repay money.
Sir Thomas has applied new limits to categories like gardening and cleaning.
Downing Street said the cleaning limit of £2,000 a year covered domestic cleaning, window cleaning, dry cleaning and laundry.
In Mr Brown's case the £12,415 ($19,614) is made up of £10,716 for cleaning claims above Sir Thomas's £2,000 annual limit, £302 spent on gardening above the annual £1,000 limit recommended and a £1,396 decorating bill that was "inadvertently assigned by error to two quarters".
A Downing Street spokesman said Mr Brown had "always supported this process and will cooperate fully and make the necessary repayment".
He added: "Mr Brown's expenses have always been cleared by the House authorities as entirely consistent with the rules. He has not claimed the maximum level of expenses. The review says its findings 'carry no implication about the conduct or motives of the MPs concerned'."
The prime minister has written to all ministers urging them "to respond promptly and in full" to Sir Thomas's findings.
He adds that they should "make appropriate repayments" where they are asked to do so.
Mr Cameron said everyone should comply with "what the authorities are asking" and added that he had received a letter from Sir Thomas.
He added: "It doesn't raise any new issues. It asks for one particular mortgage statement which of course I will provide about a particular period of time but it doesn't ask for any money to be paid back. But of course if any further request is made I will obviously meet it and meet it straight away."
Commons Speaker John Bercow has written to all MPs urging them to co-operate fully, amid reports many MPs plan to defy recommendations to repay claims that were cleared at the time.
Sir Thomas, whose final report is expected in December, does not have the power to demand that they repay money.
His report will go to the Commons' Members Estimate Committee which will decide whether to order its recommendations be carried out.
But Sir Stuart Bell, who sits on the estimate committee, told the BBC on Sunday that Sir Thomas had been asked to carry out a review "in accordance with the rules at the time and the standards that applied at the time".
"I think many MPs, if they read the newspapers, may feel [Sir Thomas] is not staying within that remit," he added.
Business Secretary Lord Mandelson said "on one level" he could understand the reaction as MPs had "honestly and fairly" made claims within the rules as they existed at the time.
"For somebody who they thought was being appointed as an auditor but is in a sense rewriting the rules... many MPs will feel today [that it is] desperately unfair," he said.
"But I think they also have to understand where public opinion is on this and, in order to bring closure to this, I think MPs will need to bite on this particular bullet, however painful."
Expenses approved by the Fees Office have been questioned since details of the claims broke and the old system is widely agreed to have been discredited.