Stapleton, an authorised representative, is alleged to have breached agent regulations.
The charge relates to Gera's switch to Fulham from West Brom in July 2008.
Stapleton is said to have acted on behalf of Fulham in the deal, having previously worked for Gera during contract negotiations with West Brom in June 2008.
In addition, Stapleton has been charged with 'failing to enter into a written representation contract with the player and/or failing to lodge the representation contract with The FA', according to a statement on the governing body's official website.
Stapleton now has 14 days in which to respond to the charge.