QPR, who beat Sheffield United 3-0 on Monday, are nine points clear at the top of the Championship, and are set for a return to the Premier League for the first time since 1996.
However, they face a possible points deduction if found guilty which could threaten the promotion which has looked a probability all season.
Faurlin joined the west London club for £4.3 million from Argentina club Instituto de Cordoba in July 2009.
Some of the charges relate to the alleged existence of an agreement between QPR and a third party in respect of the player's economic rights and the alleged failure by the club to notify the FA of that agreement before the player was registered.
QPR have also been charged with allegedly using or seeking to pay an unauthorised agent in relation to the player's registration.
West Ham were fined £5.5 million but avoided a points deduction, saving them from relegation.
Sheffield United, who were relegated, were furious and although they failed to have the decision overturned they eventually won £25 million in compensation from West Ham.
Sheffield United's manager was Neil Warnock who was fiercely critical of the FA at the time. Warnock is currently the manager of QPR.
