The Football Association have charged Emre with using racially-aggravated abusive and/or insulting words.
The charge stems from an incident during Everton's recent 3-0 win over Newcastle.
The Turkish midfielder was involved in altercations with Everton players in the first half of the game at Goodison Park on January 30, 2006.
Claims that he racially abused Everton players were included in Dermot Gallagher's report - although the referee did not hear them himself.
But the FA have been in contact with Everton since the game and have now decided to charge the player.
Emre has until 29 January to respond to the charge.