Lampard could receive a one-match suspension if he is deemed to have used insulting language or behaviour towards the official during the incident.
"Derby County manager Frank Lampard has been charged following the game against Rotherham United on Saturday," the FA said in a statement on Twitter.
"It is alleged that his behaviour in the 77th minute amounted to improper conduct. He has until 6 p.m. (1700 GMT) on Thursday to respond to the charge."
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Derby are currently seventh in the second-tier table and host 13th-placed Blackburn Rovers on Tuesday.
(Reporting by Simon Jennings in Bengaluru; Editing by Christian Radnedge)
