The 24-year-old defender was charged following an incident in Duke Street in Liverpool city centre at around 03:20 GMT on Friday.
A force spokesman said Flanagan, from Cressington, Liverpool, is accused of common assault.
He has been released on conditional bail and will appear before Liverpool City Magistrates’ Court on 2 January.
A Liverpool FC spokesman said: “The club has been made aware of an alleged incident involving a member of the first team playing squad.
“We will be making no further comment on the matter while the process is ongoing with the relevant authorities.”
Liverpool-born Flanagan has made more than 50 first-team appearances for the club since making his debut aged 18.
He was a standby for England’s 2014 World Cup squad, but has only played once for Liverpool this season and spent last season on loan at Burnley after a 20-month injury lay off.