Mudryk has not played for Chelsea since his provisional suspension by the FA for an “adverse finding in a routine urine test” in December.
The Ukraine international at the time said he was in “complete shock” and he “never knowingly used any banned substances”.
But Mudryk could face a potential ban of up to four years under FA rules.
An FA statement on Wednesday said: “We can confirm that Mykhailo Mudryk has been charged with anti-doping rule violations alleging the presence and/or use of a prohibited substance, in terms of regulations three and four of the FA’s anti-doping regulations.
“As this is an ongoing case, we are not in a position to comment further at this time.”
Signed from Shakhtar Donetsk in January 2023, 24-year-old Mudryk was reported to have had the prohibited performance enhancing substance meldonium in his positive test.
Earlier this month, Mudryk’s number 10 shirt was given to Cole Palmer for next season, leaving the Ukraine international without a squad number at Stamford Bridge.
The positive test was returned shortly after he had been away on international duty with Ukraine in November.
Chelsea boss Enzo Maresca initially said the winger was ill when asked to explain the four-game period he was absent from the team prior to the suspension being made public.
Mudryk’s time at Chelsea has been dogged by inconsistency, with erratic performances only occasionally off-set by flashes of his ability.
He has scored just 10 goals in 73 appearances in all competitions for the Blues. (AFP)
