The Football Association has charged Gillingham and their chairman Paul Scally in relation to the dismissal of former striker Mark McCammon in 2011.
An employment tribunal ruled McCammon, now 36, was sacked by the Gills in a case of unfair racial victimisation.
The club and Scally allegedly breached FA rule E3 and "failed to act in the best interests of the game, and/or brought the game into disrepute".
Both Gillingham and Scally have until 14 November to respond to the charge.
McCammon joined Gillingham in the summer of 2008 but was released three years later after scoring five goals in 62 appearances for the Kent side.
He claimed Gillingham refused him treatment for an injury, docked his wages and fined him for not turning up to training during heavy snow.
McCammon also alleged he and other black players at the club were treated differently from white players.
Scally said allegations of racism were "made maliciously and were without foundation" but an employment tribunal in Ashford, Kent, found in McCammon's favour in July 2012 and he was subsequently awarded £68,000.
Gillingham appealed against the decision but the tribunal's verdict of racial discrimination was upheld by a judge in September 2013.