The FA said in a statement that the symbol sported by the former Barcelona boss on his jacket broke its rules.
“Pep Guardiola has been charged for wearing a political message, specifically a yellow ribbon, in breach of the FA's kit and advertising regulations,” the FA statement said.
“He has until 6pm on Monday 5th March 2018 to respond to the charge.”
Following events last year surrounding Catalonia's bid to break away from Spain, which included a referendum and a proclamation of independence, both deemed illegal, authorities jailed several leaders of the movement.
The City manager, who was born in Catalonia, has previously explained his reasons for wearing the ribbon.
Referring to the first two independence leaders to be jailed, he said in December: “I do that because in Spain two specific people who defend something like the vote, something the people in command do not agree (with), are in prison. It's unfair.
“To make a rebellion on something like that, you have to be something tough to be in prison. And they are still there. So, while they are not out, always here (points to ribbon) will be shared with me.
“Because, OK, they can suspend me for doing that, but the other people are in jail. If they want to suspend me — UEFA, Premier League, FIFA — it's OK.”
The City boss explained his stance in response to comments from Manchester United manager Jose Mourinho, who questioned whether the ribbon was within the rules and claimed he would not be allowed to do a similar thing.
Last year world governing body FIFA backed down in its row with British football authorities over the wearing of poppies, worn to remember war dead.
England, Scotland, Wales and Northern Ireland had previously been fined by FIFA for wearing or displaying poppies, which FIFA said were “political symbols”.
FIFA's climbdown meant none of the British home nations had to pay their fines.
Guardiola's Manchester City team face Arsenal in the League Cup final on Sunday. Victory would bring Guardiola's first silverware as City boss after a trophy-laden managerial career with Barcelona and Bayern Munich.