The FA claimed that Mourinho swore in Portuguese to a television camera as he walked off the pitch following a 3-2 win over Newcastle on 6 October.
However, United successfully contestedthe original charge.
The FA’s appeal comes after considering the written reasons of the Independent Regulatory Commission inquiry.
English football’s governing body had expressed surprise at the decision to clear Mourinho, made by the three-person panel, after they had used a lip reader to support the case that his remarks were offensive.
A TV camera filmed the Portuguese appearing to say something, and make a gesture with his right hand, as he walked off the pitch following his side’s win over the Magpies.
Mourinho is facing a touchline ban if that decision is overturned and he is found guilty of the charge.