The club unveiled a new heavily branded kit in July, which featured a large Paddy Power logo in a sash across the front, prompting scathing criticism.
The kit was worn in a pre-season friendly, before being revealed as part of a stunt that would launch the Paddy Power campaign calling for the removal of gambling shirt sponsorship in football.
Paddy Power, owned by Flutter Entertainment, then confirmed this season’s Huddersfield kit would not include its logo.
In donning the design for an official match, the club is seen to have breached a section of the FA’s kit and advertising regulations, stipulating that a kit is permitted to have "one single area not exceeding 250 square centimetres on the front of the shirt."
Huddersfield has until 16 August to respond to the charge, expected to result in a fine.
Paddy Power has agreed similar deals this season to "unsponsor" the shirts of Newport County, Motherwell, Macclesfield Town and Southend United.
