The United manager spoke into a camera after his side came from behind to triumph 3-2 at Old Trafford.
The FA alleges Mourinho's language was "insulting and/or abusive and/or improper".
An FA spokesperson said: "Jose Mourinho has been charged following Manchester United's game against Newcastle United on October 6, 2018.
"It is alleged that his language at the end of the fixture, as captured by the broadcast footage, was abusive and/or insulting and/or improper. He has until 6pm on October 19, 2018 to respond to the charge."
BREAKING: José Mourinho has been charged following Manchester United’s game against Newcastle United on 6 October 2018. pic.twitter.com/r6rQosYa2w
— Sky Sports News (@SkySportsNews) October 16, 2018
Mourinho could potentially face a touchline ban if found guilty.
The match was played amid a tense atmosphere with the club having denied a report earlier in the day that Mourinho was going to be sacked that weekend regardless of the result.
United recovered from 2-0 down to complete a dramatic comeback with a 90th-minute goal from Alexis Sanchez.
Footage from the game shows Mourinho saying something - at one point while looking into a camera - as he headed towards the tunnel following the final whistle.