The charge relates to Warnock's conduct following his side's clash at Millwall on November 18.
The Whites boss blasted referee Mark Halsey in his post-match comments after he dismissed Luke Varney in the 1-0 defeat at The Den. Varney was sent off just three minutes into the second half for an apparent elbow on Adam Smith.
Warnock said: "The amount of effort that's gone into the game and we're talking about a refereeing decision - it's scandalous. When you watch the sending-off again, we don't have thousands of Millwall fans screaming at us. It's not caught him where he's holding when he's gone down.
"Referees aren't as consistent - they've gone backwards, I think. I didn't think someone of Mark Halsey's quality and experience would have gone straight for his red card, and I think he'll be disappointed when he sees it, but that will do us no good."
The 63-year-old has until 4pm on Friday to respond to the charge.