UEFA disclosed this in a statement on Tuesday.
England lost 3-2 to Italy on penalties, but the occasion was tarnished by violence both inside and outside Wembley.
Before the match kick-off, supporters without tickets forcefully stormed several entrances at the stadium.
Many fans reported that their seats had been taken by intruders, which sparked escalated and violent exchanges inside the stadium.
UEFA’s statement partly read: “Disciplinary proceedings have been opened following the UEFA EURO 2020 final match between the national teams of Italy and England (1-1, Italy won 3-2 on penalties), played on 11 July at Wembley Stadium, London.
“Charges against The English Football Association:
“Invasion of the field of play by its supporters – Article 16(2)(a) of the UEFA Disciplinary Regulations (DR);
“Throwing of objects by its supporters – Article 16(2)(b) DR;
“Disturbance caused by its supporters during the national anthem – Article 16(2)(g) DR;
“Lighting of a firework by its supporters – Article 16(2)(c) DR.”
Meanwhile, the FA also received a €30,000 (£26,000) fine from UEFA following the disturbances during the semi-final against Denmark at Wembley.