Aguero has until Wednesday evening to respond to the charge, which comes after he appeared to swing an elbow at West Ham defender Winston Reid during City’s 3-1 win in the Premier League on Sunday.
If found guilty, the Argentina striker can expect a three-match ban that would rule him out of the showdown with United at Old Trafford on 10 September, a subsequent league visit from Bournemouth and an EFL Cup tie at Swansea.
Referee Andre Marriner reported that he did not see the clash between Aguero and Reid, who left the field clutching his throat moments later, and that confirmation opened the door for the FA to begin the process of taking retrospective action.
A panel of three former referees reviewed video footage of the incident and agreed unanimously that Aguero should be charged.
The City forward’s absence would be a major fillip for United and their new manager Jose Mourinho, who has a long-standing and bitter rivalry with City coach Pep Guardiola from their respective tenures at Real Madrid and Barcelona.
Aguero has already scored six times in four appearances this season and helped City to set the Premier League pace by taking nine points from a possible nine. United also have a 100 per cent record, as do Chelsea.
The former Atletico Madrid star, 28, has been withdrawn from the Argentina squad for their forthcoming World Cup qualifying matches with a calf injury.
His absence would leave Guardiola to choose between Kelechi Iheanacho, Wilfried Bony or Raheem Sterling to spearhead their attack in the derby.