Birmingham were hit with a charge of failing to ensure fans conducted themselves in an orderly fashion during the Championship fixture against bitter rivals Aston Villa on Sunday.
Villa captain Jack Grealish was punched and knocked to the turf by a Birmingham fan in the ninth minute of Sunday's 1-0 victory over the Blues in the 'second city' derby at St Andrew's.
"Birmingham City FC has been charged with breaches of FA Rule E20 (a) and (b)," an FA statement said.
"It is alleged the club failed to ensure that its spectator[s] conducted themselves in an orderly fashion; refrained from improper or violent conduct and refrained from encroaching onto the pitch during the EFL Championship fixture against Aston Villa on Sunday. They have until 22/03/2019 to respond.".
Birmingham fan Paul Mitchell, 27, was subsequently jailed for 14 weeks for his attack on Grealish after pleading guilty to assault and invading the pitch.
He was also banned from all football stadiums for 10 years by Birmingham Magistrates' Court, while Blues imposed a lifetime ban from their fixtures.
Arsenal were also charged in connection with an incident in which a spectator ran on to the pitch during Sunday's Premier League win over Manchester United.
After Arsenal's Pierre-Emerick Aubameyang sealed a 2-0 victory with his second half penalty, the fan barged past United defender Chris Smalling.
A 30-year-old man has been charged with common assault and bailed to appear at Highbury Corner Magistrates' Court on March 26.
"Arsenal FC has been charged with breaches of FA Rule E20(a)and (b)," the FA said.
"It is alleged the club failed to ensure that its spectator[s] conducted themselves in an orderly fashion and refrained from encroaching onto the pitch during the Premier League fixture against Manchester United on Sunday. They have until 22/03/2019 to respond."