The Pride Park-club were handed the points penalty after entering administration in September following ongoing financial trouble.
The English Football League announced on Monday the appeal had been lodged and said the matter would now be referred to an independent arbitration panel.
The points deduction, which was imposed following the club confirming the appointment of administrators on September 22, will remain applied to the Championship table while the arbitration process is ongoing, the EFL said.
The league’s regulations state an appeal against the penalty can only be launched on the grounds of ‘force majeure’ – where a club enters administration due to “unforeseeable and unavoidable” circumstances.
Timeline of Derby County takeover and how this has unfolded so far this year:
7 April - Sale of Derby to Spanish businessman Erik Alonso's No Sports Limited agreed
14 May - Erik Alonso's attempt to buy Derby
24 June - Derby fined £100,000 because of the club's accounting policies
22 September - Derby hit by automatic 12-point deduction
23 September - Wayne Rooney says he's 'disappointed' over lack of communication
11 October - Derby appeal against points deduction imposed on 22 September
A club statement was issued on September 17 saying the intention was to enter administration.
It said the coronavirus pandemic had "a severe impact" on revenues and that the club had become unable to service its day-to-day financial obligations.
Derby’s administrators rated the club’s chances of avoiding liquidation at 95 per cent last month, and said at the time they were already aware of six parties interested in buying the club.
On the pitch, the Rams are on two points with the 12-point deduction applied, seven off safety.
However, they face the prospect of a further, separate points deduction over breaches of EFL financial regulations under their former owner Mel Morris.