The Millers played Farrend Rawson in the win over Brighton on 6 April, a day after his youth loan had expired.
Rotherham are now just one point above the Championship relegation zone with three games left.
A club spokesperson said: "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," it said.
"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."