It is alleged his post-match remarks constitute improper conduct in that they allege and/or imply bias on the part of the match official, and/or bring the game into disrepute, in contravention of Rule E3(1).
He has until 6pm on Thursday 8 October 2015 to respond to the charge.
Neil Lennon was quoted as saying:
"He was a disgrace, and absolute disgrace,"
"I have not seen a more biased performance from a referee in a long, long time. He gave QPR everything he possibly could. "I was so frustrated with that.
"Any 50-50 challenges the free kick would look like it was going to us and he invented a free-kick for QPR. "
Neil Lennon has previously been warned on his conduct, after being sent to the stands in his first match as Bolton boss, away at Birmingham City last October.