The charge alleging misconduct refers to the transfer of Ross McCormack to Fulham in July 2014, the FA said in a statement.
Scottish striker McCormack left Elland Road in a deal worth around £11m.
Owner Massimo Cellino and authorised agent Derek Day have been charged and have until May 20 to respond.
The FA said on its website: "Leeds United have been charged for breaching the FA's football agent regulations
The alleged misconduct relates to the transaction involving the transfer of Ross McCormack from Leeds to Fulham on 8 July 2014."
The club declined to comment when approached by Press Association Sport.
McCormack spent four years at Leeds before being sold to Fulham and the Scotland international claimed at the time that he was "hung out to dry by the club".
He said that Leeds would "always have a special place in my heart" but was "no longer the Leeds United I fell in love with".
Cellino's FA charge is the latest in a long list of controversies to hit the former Cagliari owner.
The Football League has yet to confirm whether his latest 223-day disqualification for a tax offence in Italy still stands after reports in his homeland that he had been acquitted by the Italian Court of Appeal over the non-payment of VAT on an imported Range Rover.
Cellino has been at odds with the Football League since the game's governing body tried to block his takeover of Leeds in 2014 after he had been convicted of another tax offence in Italy.
He later served a four-month ban in the second half of last season, imposed by the Football League after it had been confirmed in an Italian court his offence had been a dishonest act.
More recently Cellino's son Edoardo, a Leeds director, was suspended by the Football Association from all football-related activity for three matches following comments he made on Facebook after getting involved in an abusive row with a supporter.
Cellino's other son, Ercole, stepped down from his position on the Elland Road board earlier this month
He resigned on March 28 but it was not announced until after he had apologised to the club's fans for causing offence by using a Nazi reference to describe his haircut in a post on Instagram.
The continued controversies appeared to have taken their toll on a weary Cellino last week when he told The Times he wished he had never bought the club and again stated his desire to leave Elland Road.
Source : PA
Source: PA