The 27-year-old, who also plays for the French national team, is due before Chester Magistrates’ Court.
He is accused of four counts of rape and one count of sexual assault, a spokesman for Cheshire Police said.
The force said the charges relate to three complainants, over the age of 16, and are alleged to have happened between October last year and this month.
A police spokesman said: “Cheshire Constabulary and the Crown Prosecution Service would like to remind everyone that criminal proceedings against Mendy are live and that he has a right to a fair trial.”
In a statement, Manchester City said: “Manchester City can confirm that following his being charged by police today, Benjamin Mendy has been suspended pending an investigation.
“The matter is subject to a legal process and the club is therefore unable to make further comment until that process is complete.”