The airline has struck a three-year deal that will ensure it has a presence in top-flight football after the end of its Chelsea shirt sponsorship in May 2005.
From this season, the Fly Emirates logo will appear on the sleeves of all referees and assistants at Barclays Premiership games. Officials at Coca-Cola Football League games and tournaments including the FA Cup and Carling Cup will also carry the identity on their strips.
The airline will invest in training officials at all levels of the game.
It follows a similar deal for Scottish football struck by Specsavers in 2001.