Federal authorities say that Louisville Metro Police Officer Cory Evans hit the person as they were kneeling with their hands in the air and surrendering to arrest.
The officer faces one count of deprivation of rights, which carries a maximum prison sentence of up to 10 years and a fine.
Charging documents filed by the US Attorney’s Office for the Western District of Kentucky state that the incident took place on or around 31 May 2020.
The victim of the alleged attack is referred to only as “MC” in the court papers and no further details are given of the “bodily injury” they suffered.
Prosecutors wrote that the officer “struck MC in the back of the head with a riot stick while MC was kneeling with hands in the air, surrendering for arrest.”
It is not the first time that Officer Evans has been accused of attacking a member of the public, according to The Courier Journal newspaper.
He was sued in August 2019 over a 2018 incident in which he is accused of repeatedly punching Jarrus Ransom after he was pulled from his car during a traffic stop in the city.
A lawsuit in that case, which also involves two other officers, is still making its way through the federal courts system.
Louisville’s police department has been under heavy focus since the killing of Ms Taylor, a Black woman, during a bungled raid by officers.
One officer in the case has been fired and charged with endangering people in a neighbouring apartment, but no one has been charged with killing Ms Taylor.
That officer has pleaded not guilty and will face trial next year.
The May protests were so large that the state’s governor, Andy Beshear, called in the National Guard to support LMPD and to enforce a nightly curfew.
In April US Attorney General Merrick Garland announced a Justice Department investigation into the practices of LMPD.
The FBI is investigating multiple other LMPD officers, according to The Courier Journal.