The Millers were sanctioned last week for playing on-loan Derby defender Farrend Rawson in their 1-0 win on Easter Monday and a three-man disciplinary commission has upheld the charge and docked them three points.
That decision plunges Steve Evans’ side deep into a Championship relegation fight, leaving them just one point above third-bottom Millwall and two clear of Wigan with a tough fixture against promotion-chasing Norwich to come on Saturday.
However, victory against the Canaries would see Rotherham secure their place in the Championship for another season providing Millwall and Wigan lose to Derby and Wolves respectively.
The club has also been fined £30,000, half of which will be suspended until the end of the 2015/16 season.
A statement on the club’s official website confirmed its intention to appeal, which must be done by May 1.
“Rotherham United FC are very disappointed by the decision to deduct three points for fielding a player who was ineligible purely because of an administrative error,” it read.
“It is our view that true sports fans want to see competitions settled on the pitch and not to have them affected by what happens in disciplinary proceedings.
“We await the reasoned judgement of the FDC and once we have received it we will issue our appeal after discussion with Jim Sturman QC.
“In the meantime we are confident that our team possesses the will and spirit to ensure that the points deduction is academic by securing our Championship status on the pitch. It would not be appropriate to make any further comment on this matter until after the appeal process has been concluded.”