Curtis Good, on loan at the club from Newcastle United, played in Bradford's second-round tie against Brentford, which ended 1-1, but the League Two side had not received written permission for him to play by a 1200GMT deadline on the day of the game.
Bradford could appeal against the decision, but if they are unsuccessful, Brentford will take their place in a third-round match with either Bury or Southend United.
"The FA has confirmed that Bradford City have been removed from The FA Cup with Budweiser 2012-13 competition after fielding an ineligible player in their Second Round tie against Brentford," read an FA statement.
Bradford said the mistake was "of an administrative technical nature" and have apologised to their fans.
"We are clearly disappointed by this decision and cannot comment further on this matter as the club is still actively conducting a full investigation," they said in a statement.
"The club has until 5:00pm today (Friday) to lodge an appeal with the FA and we are currently reviewing our position in relation to this."
Source: AFP
Source: AFP