The Portuguese was sent to the stands during his side's 1-0 defeat at Aston Villa on March 15 following his response to Ramires's late sending-off for a challenge on Karim El Ahmadi.
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The midfielder's dismissal was Chelsea's second of the match after Willian was sent off for two yellow cards earlier in the Premier League encounter.
Mourinho had earlier stated his intention to contest the charges, telling the press on Friday: "Yes, I have decided. I don't accept the charges.
"I will [make my defence] privately but, for obvious reasons, I don't accept the charges."
The FA confirmed to Perform on Tuesday that Mourinho had denied the charge and requested a personal hearing.