The 26-year-old missed the Ashes series in Australia as a consequence of the incident, with the England and Wales Cricket Board opting to rule him out.
The Crown Prosecution Service said in a statement: “The CPS was passed a file of evidence by Avon & Somerset Police on November 29, 2017 in relation to an incident of disorder in Bristol city centre.
“Further material was subsequently received in late December.
“Following a review of all the available evidence, the CPS has today authorised the police to charge three men with affray in connection with the incident.”
Avon and Somerset Police added in a statement: “Three men have today been charged in connection with an incident of disorder on Queens Road, Bristol on September 25 last year.
“Having carefully considered the evidence, the CPS has today authorised Ben Stokes, 26, of Durham, Ryan Ali, 28 and Ryan Hale, 26, both of Bristol, to each be charged with one count of affray.
“They will appear at Bristol Magistrates’ Court at a date to be confirmed.”