Manchester United have denied any wrongdoing in the signing of goal keeper Tim Howard last summer.
United have been forced to defend themselves against allegations of improper conduct in the when they signed Howard from NNY Metrostars.
The FA will investigate after being sent documents showing alleged breaches of their rules by the Sunday Times newspaper.
However, United will vigourously defend their conduct.
“All our deals are approved by the board of Manchester United PLC and are conducted in accordance with Fifa and FA rules,” said a club statement.
“Details of payments involved in those deals are sent to the football authorities as required under their regulations.”
Meanwhile, the FA’s compliance unit is to look at the deal which saw Howard arrive in July.
“Various documents are now in our possession,” confirmed David Davies, the FA’s executive director.
“They will be studied very carefully and any breach of the rules and regulations that they show will then be discussed as a matter of urgency.”
Jason Ferguson’s Elite Management agency, run by the son of United manager Sir Alex, is at the centre of the current allegations, primarily because of the role reportedly played by Mike Morris, a Monaco-based agent with close ties to Elite.
According to claims in the Sunday Times, Morris received £139,000 commission from a Swiss agent, Gaetano Marotta, who United had authorised to negotiate the Howard transfer.