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.
QPR have denied all the charges against them.
In a statement, the FA confirmed the charges relate to the player Alejandro Faurlin (pictured), who scored a stunning goal against Sheffield United.
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.
FALSE DOCUMENTS
QPR have also been charged with allegedly using or seeking to pay an unauthorised agent in relation to the player's registration.
QPR and club chairman Gianni Paladini are also charged with submitting false documents to the FA when Faurlin signed an extension to his playing contract in October.
QPR and Paladini have indicated they are denying all of the charges and will be contesting them at the hearing, which should return its verdict by May 6, just before the last Championship match of the season on 8 May.
The case has similarities to that of Argentines Carlos Tevez and Javier Mascherano, whose arrival at West Ham United in 2006 sparked a series of court cases and inquiries and led to the FA changing its rules on third-party ownership.
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.
