The Manchester City manager began wearing his ribbon after Jordi Sanchez and Jordi Cuixart were placed in custody as part of the crackdown that followed last October's referendum on Catalan independence – a poll the national government in Madrid deemed to be illegal.
"Pep Guardiola has been charged for wearing a political message, specifically a yellow ribbon, in breach of The FA's kit and advertising regulations," An FA statement read. "He has until 6pm on Monday, March 5 to respond to the charge."
City will play three games before that deadline – the Carabao Cup final against Arsenal, a trip to the Emirates Stadium to face the Gunners in the Premier League on Friday (AEDT) and Chelsea's visit to the Etihad Stadium next weekend.
Guardiola has been a vocal proponent of Catalan independence and the FA charge was the second time his political alignment placed him in the headlines.
Speaking at a news conference to preview the Carabao Cup final, the ex-Barcelona boss confirmed Spain's Guardia Civil had searched his family's private plane when it landed at El Prat airport earlier this week. Reports in Spain claimed the law enforcement officials were looking for former Catalan president Carles Puigdemont, who has been living in exile in Belgium since October.
"That's something that my wife explained to me. It happened like it's being published in the news," Guardiola said.
Ahead of December's derby match at Old Trafford, Manchester United manager Jose Mourinho suggested Guardiola was receiving preferential treatment by not being subjected to FA sanctions for wearing the yellow ribbon.
After his side beat United 2-1, Guardiola responded by stating he would be willing to take a suspension for supporting his cause.
"I do that because in Spain two specific people who defend something bold are in prison. It is unfair," he said. "To rebel like that, you have to be something tough to be in prison, and they are still there. Until they are out, always they will be with me.
"They can suspend me for that but the other people are in jail.
"Jordi Cuixart and Jordi Sanchez are in prison without their families. They want to suspend me - UEFA, the Premier League, FIFA - it's OK. I will be suspended."