The club said their officials dealing with the paperwork would be heavily involved on Wednesday with transfer negotiations, so the FA had agreed to an extra day's grace.
They now have until 1700 GMT on Thursday to decide whether to appeal.
Aguero was charged following an incident involving West Ham defender Winston Reid during Sunday's Premier League match at the Etihad Stadium.
If he is found guilty, the Argentine striker will miss three matches, including the local derby against Manchester United on Sep 10.