The United defender will have a hearing today to decide whether he will face a ban following an off-the-ball incident in United's 4-0 victory over Hull City on Saturday.
A statement on the FA website said: "Manchester United defender Rio Ferdinand has denied a charge of violent conduct.
"The charge relates to an incident involving Hull City forward Craig Fagan during the second half of the match at Old Trafford. A Regulatory Commission will hear the charge on Thursday 28 January."
Ferdinand's decision to deny the charge meant he was eligible to play against Manchester City in the Carling Cup semi-final on Wednesday.
Sir Alex feels optimistic about the outcome. He said: "If it’s a fair hearing then he has a good chance. He was wrestled and punched, all sorts of things happened to him, and he was just trying to wrestle free from it. Unfortunately for us he’s caught him [Fagan] on the back of the head. But we will contest it."