The FA confirmed on Thursday they had charged Bruce following remarks he made to the media after his side's 1-0 Premier League defeat at Tottenham.
Bruce was unhappy with the decision to award Spurs a penalty, which Roberto Soldado scored to give the home side the points.
Referee Michael Oliver adjudged that Ahmed Elmohamady had handled the ball in the box after the ball ricocheted off his legs and onto his arm - a decision Bruce branded a "joke", adding: "I have to ask the question, would we have got it? In my opinion, he (Oliver) couldn't wait to give it."
After Hull's second defeat to Spurs in the space of four days, in the Carling Cup on Wednesday, Bruce revealed he had already been informed he would be charged by referees chief Mike Riley, who also admitted to the former Sunderland boss that Oliver had made an error in awarding the spot kick.
"I've been charged," Bruce said. "Mike Riley rang me on Monday morning telling me they've made a huge mistake. What am I supposed to say?
"I thought the referee today was tremendous. We like to see what we've witnessed today and let's not lose that. What is the law and what is it supposed to be? I'll argue my case. It will cost me a few quid, but I'll do it."
A statement on the FA website read: "It is alleged Bruce's comments called into question the integrity of the match referee, and/or implied that the match referee was motivated by bias; and/or brought the game into disrepute, in contravention of Rule E3(1)."
Bruce has until 6pm on 4 November to respond to the charge.