Merseyside Police said the 24-year-old full-back had been charged following an incident in Liverpool city centre on Friday.
A force spokesman said: "Merseyside Police can confirm that Jonathan Patrick Flanagan, aged 24, from Cressington in Liverpool has been charged with Section 39 common assault following an incident on Duke Street in Liverpool city centre at around 3.20am on Friday December 22.
"He has been released on conditional police bail and will appear before Liverpool City Magistrates' Court on January 2 2018."
Flanagan came through Liverpool's academy system and made his senior Reds debut in 2011, though he has played just once this season in the Carabao Cup.