The Football Association have charged Newcastle midfielder Emre with "using racially-aggravated abusive and/or insulting words" during the match against Everton at Goodison Park last month.
Turkish international Emre was involved in angry exchanges with Everton players during The Toffees' 3-0 win on 30th December.
Everton players took exception to Emre appearing to wave an imaginary card after Leon Osman had felled Kieron Dyer in the box and a melee ensued.
The incident was mentioned in referee Dermot Gallagher's report and, following a thorough investigation, The FA have opted to charge Emre.
The Turkish international has until 29th January to respond to the charge.