Gillingham and their chairman Paul Scally have been fined £75,000 each for "race victimisation", the Football Association has announced.
The charges arose after an employment tribunal ruled striker Mark McCammon had been unfairly dismissed by the League One club.
A tribunal found McCammon's sacking was an act of racial victimisation.
Scally said he was "shocked, stunned and angered" and confirmed he and the club would appeal against the decision.
McCammon, now 36, was sacked by the Gills in January 2011 and alleged he and other black players at the Kent club were treated differently from white players.
An employment tribunal found in favour of McCammon and awarded him £68,000 in damages in August 2012, and upheld that decision a year later following an appeal by the Gills.
The FA charged Gillingham and Scally with bringing the game into disrepute last September, and a regulatory commission considered the charge at a two-day hearing in April.
Along with the fines, Scally has been ordered to attend an education programme.
Scally said the level of the fines handed out by the FA were "manifestly excessive, totally disproportionate and completely unjust".
"We have been given no reasoned explanation for the severity of the fines," he said in a statement on the club website.
"The club and I will be appealing against this decision and, if necessary, we will take the matter beyond the FA."