Mourinho’s charge for alleged abusive language following last month’s game between Manchester United and Newcastle was found not proven.
The United manager requested a non-personal hearing and the club said they presented a strong defence against the FA’s charge which was dropped by an independent panel.
The FA said: “Having carefully considered the written reasons of the Independent Regulatory Commission relating to the case involving José Mourinho, The FA can confirm it is appealing the decision.”
In those written reasons, the independent commission hired a Portuguese language expert to determine what Mourinho said into a television camera following the 3-2 win at Old Trafford.
Mr Pedro Xavier concluded the words said in Portuguese would offend in a literal sense but said the phrase used by Mourinho could have been a term used in a non-offensive way.
The FA say they do not accept that reasoning and believe Mourinho used the words to cause offence.