The charge, which comes two months after Ferguson received a five-match touchline ban for criticising referees, relates to views expressed at a news conference before last Sunday's 2-1 victory over Chelsea.
FA regulations make it clear that managers are not allowed to comment on referees before a match, regardless of whether the statements are positive or negative.
"Manchester United manager Sir Alex Ferguson has been charged with improper conduct. The charge relates to media comments made about match official Howard Webb on May 6," the FA said in a statement.
"Ferguson has until 4pm on May 16 to respond to this charge."
Ferguson's previous misconduct charge from English soccer's governing body came after he said he "feared the worse" when he found out Martin Atkinson was refereeing United's match at Stamford Bridge in March, which his team lost 2-1.
"He's definitely the best referee in the country, there is no doubt about that," Ferguson replied. "I think we're getting the best referee.
"We hope it's our turn for a little bit of luck."
Ferguson had spoken before about refereeing decisions seeming to go Chelsea's way, saying after April's Champions League quarter-final first leg that he felt no guilt when the referee failed to award the London side a penalty as United had waited years "to get a decision" at Stamford Bridge.
Arsenal manager Arsene Wenger was surprised at Ferguson's latest charge and offered a light-hearted reason for it.
"They are not used to him being complimentary, it was a shock to the FA," he joked at a news conference.
"It doesn't look very serious... I wouldn't charge him for that."
