The charge, which could lead to a three-match ban, came after a video review panel re-examined footage during which Cisse elbowed defender Seamus Coleman at St James' Park on Sunday.
The incident was unseen by the match officials.
Everton manager Roberto Martinez called the failure to punish Cisse "unacceptable", saying the Senegalese attempted to "hurt" Coleman.
Cisse equalised a minute later for Newcastle who went on to win 3-2.
"Those are not actions we want to see on a football pitch and the referee should have seen it," Martinez said.
(Writing by Ian Chadband, editing by Tony Jimenez)
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