The Portuguese had until Monday to respond to a separate FA charge of misconduct over comments about referee Anthony Taylor
The Portuguese, no stranger to disciplinary hearings during his two spells at Chelsea, had until Monday to respond to a separate Football Association charge of misconduct over comments about referee Anthony Taylor ahead of United's recent goalless draw against arch-rivals Liverpool.
But Saturday's incident at Old Trafford threatens to land Mourinho with a far more severe punishment.
Mourinho was sent to the stands at half-time for protesting too vehemently to the officials, having seen Matteo Darmian denied what the United boss felt was a penalty.
United finished the match with 10 men after midfielder Ander Herrera was sent off in a result that added to the growing pressure on Mourinho, with the Red Devils without a win in four league games and eight points behind the leaders.
While a fine appears the most likely penalty for his comments about Taylor, Mourinho could be hit with a one-match touchline ban, as well as a fine, if the FA find he used insulting and/or abusive language towards referee Mark Clattenburg at Old Trafford.
If Mourinho appeals and that appeal fails, he could be sidelined from the dug-out for two games.
Mourinho failed to attend the post-match press conference that followed the Burnley draw, with assistant Rui Faria speaking to reporters instead.
Asked why Mourinho had been sent to the stands, Faria said: "I don't know and I don't think it is really important. I think what is important is what the referee will write in his report. I can't give you more details."