In September, Stevenage said that racism allegations surrounding their caretaker boss had “no foundation”, after conducting their own investigation.
He is accused of having made the remark to a coach who used to work with the Sky Bet League Two club earlier this season and it was alleged that the comment was aimed at a player during a conversation about transfer targets.
Sampson, who was named as the interim manager at the League Two side following the dismissal of Dino Maamria earlier this season, denies the accusations.
An FA statement read: “Mark Sampson has been charged with a breach of FA Rule E3.
“It is alleged that a comment made by the Stevenage FC caretaker manager breached FA Rule E3(1) as it was improper and/or abusive and/or insulting.
“It is further alleged that the comment also constitutes an ‘aggravated breach’, which is defined in FA Rule E3(2), as it referenced ethnic origin and/or colour and/or race and/or nationality.
“He has until 6 December 2019 to provide a response to the charge.”
The 37-year-old was relieved of his duties as England Women boss in 2017 after bullying and discrimination allegations.
He was also alleged to have had a relationship with a player during his time as a coach at Bristol Academy.
Former Lionesses forward Eniola Aluko said she has forgiven former boss Sampson, following her claims of racism, harassment and bullying in the Lionesses camp.