Wirral official Dean was left bleeding from an injury above his right eye during the game between Cardiff and Swansea.
The incident happened in the 42nd minute of Sunday's Championship clash at Ninian Park.
Dean needed medical treatment for the injury he suffered in the 2-2 draw.
South Wales Police confirmed today a 24-year-old man from Pontypridd has been charged in connection with a missile-throwing incident.
He was released on bail to appear at Cardiff Magistrates Court on April 20.
Police made six other arrests outside the ground after the match, five relating to public order offences and one for breaching a football banning order.
Of those involved, three were from Cardiff, one from Ebbw Vale, one from Blackwood and one from Abertillery.
The Football Association of Wales have confirmed they are also investigating the incident.
Cardiff, who have been plagued by a hooligan reputation in the past, could now face further punishment from the FAW, although the association have refused to put a timescale on when a decision will be made.
Meanwhile, referees body PGMO (Premier Game Match Officials) have confirmed the matter is now in the hands of the FAW and the police.
A statement read: "Mike Dean was well looked after by the medical staff at Cardiff City after being injured by a coin thrown by a spectator.
"The matter is in the hands of the Police and the referee has filed his report with the Football Association of Wales."