Conservative MP Stewart Jackson is being sued by the Independent Parliamentary Standards Authority (Ipsa) for refusing to pay back £54,000 which he claimed on expenses.
All other MPs who made a profit after claiming expenses to pay their mortgages have agreed to pay back hundreds of thousands of pounds to the taxpayer.
Ipsa published details of repayments by 71 politicians on its website.
But Mr Jackson has refused to pay the money back so Ipsa have filed papers with the High Court to sue him.
The Tory MP for Peterborough has vowed to fight the legal proceeding, accusing the watchdog, which was set up in the wake of the 2009 MPs' expenses scandal, of being "heavy handed and disproportionate".
He said the court action was "intended to bully me into submission".
When Ipsa took up the role of Parliamentary watchdog in 2010 they changed the rules so that MPs could not claim for mortgages on their second home. This was designed to prevent politicians from profiting - essentially gaining a home or asset paid for by the state - when they leave office.
Transitional arrangements were put in place permitting MPs elected before 2010 to keep claiming the money up to last August - as long as they agreed to return any potential capital gain.
Valuations were taken of the properties in 2010 and 2012 and the money owed by way of capital gains between the two dates has to be paid back.
But Mr Jackson is challenging the valuation on his house, claiming that even if it rose by £54,000 between 2010-12, it is actually worth less now than when he bought it in 2005.
Stewart Jackson is the only MP so far not to have reached a deal with IpsaIn a statement, he said: "Ipsa are seeking a cash sum on a so-called capital gain "profit" on my family home, in which I live and have not sold.
"The money which Ipsa is demanding retrospectively is more than the total amount I received when I was claiming mortgage interest and the property is now valued at less than we purchased it for in 2005.
"Their assumption is that the value of my property rose by almost 20% over two years whilst house prices fell by 3% in my constituency in the same period.
"At my own expense, I have paid for an accurate recent expert valuation and I have made a reasonable offer to Ipsa to settle the matter and reduce the legal costs which will have to be met by the taxpayer."
The watchdog said the valuations were conducted independently by the Royal Institution of Chartered Surveyors (RICS).
The sums published by Ipsa range from a few hundred pounds in some cases to the £81,446 paid by Tory MP for Clwyd West David Jones and the £61,403 returned by DUP East Londonderry MP Gregory Campbell - both for properties in London.
Defence Secretary Philip Hammond had owed £34,833 and Treasury Minister David Gauke £26,762.
Mr Stewart added: "Ipsa have negotiated with 70 other MPs in a secretive and arbitrary manner but in respect of my case, regrettably, they have refused to negotiate.
"I am merely seeking fair play and consistency and will pursue legal action to receive it."
In total the 70 MPs have been asked to hand back almost £500,000 worth of profits from taxpayer-funded homes, although some MPs do not have to return any money because the value of their property was judged to have not changed.
MPs are allowed to put in place payment plans so they do not have to pay back the money in one lump sum.