Guardiola has said he wears a yellow ribbon to support imprisoned pro-independence politicians in his native Catalonia.
The FA ruled it breached their rules on kit and advertising regulations.
Guardiola said in November: “If one day in prison was already too much, look how many days they've been there now.
“Like everybody knows, hopefully sooner or later I can stop wearing it.”
The 47-year-old has been wearing the ribbon in support of the political leaders jailed following the Catalonia independence referendum last October, which was declared illegal by Spain.
An FA statement read: “Manchester City manager Pep Guardiola has admitted an FA charge for wearing a political message, specifically a yellow ribbon, in breach of the FA's kit and advertising regulations. A paper hearing has been requested, with a date to be set in due course.”
His much-publicised stance over the controversy in Catalonia has become a major issue in his homeland where, according to reports in Spain, the City manager's private plane was searched at Barcelona's El Prat airport two weeks ago by police looking for exiled Catalan leader Carles Puigdemont.
Since the charge was issued Guardiola has either covered up the ribbon during games or not worn it.
However, Guardiola insists that, even though his protest aims to highlight the fates of a jailed group that includes Catalan politicians Jordi Sanchez and Jordi Cuixart, it is not a political issue.
“When men and women put on a pink ribbon it's because of the support for the breast cancer initiative,” he said.
“The same when I wear the the prostate cancer badge, it's the same, the idea is the same, there are a lot of ribbons.
“I'm pretty sure there are people all around the world in Spain and Catalunya who do not want to be independent, but they are not agreeing with putting people in 'prevention' jail.
The FA's stance on the matter differs from European governing body UEFA, who allow the ribbon to be worn. City also believe the symbol is not generally considered offensive
The yellow emblem worn by Guardiola during Sunday's Premier League win over Chelsea was the daffodil of the Marie Curie cancer charity.