Albion have pledged their continued cooperation with the FA after being charged.
The club are alleged to have committed several breaches of regulations on working with intermediaries between January 2015 and January 2018.
Albion have two weeks in which to respond.
They have revealed they themselves reported "historical administrative errors" and have co-operated fully with the FA throughout.
A club statement read: "Following an internal review in 2019, Brighton and Hove Albion identified and self-reported to the FA a limited number of historical administrative errors relating to the processing of paperwork for intermediaries between 2015 and 2018.
"The club has openly co-operated with The FA throughout since initially raising the issue with them and will continue to do so.
"No further comment will be made at this time."
The section under which Albion have been charged relates to concealing or misrepresenting “the reality and/or substance of any matters in relation to a transaction.”
The term “intermediaries” replaced the licensing system for agents in 2015.
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