The 24-year-old defender was arrested by police at around 3.20am last Friday after being called to an incident on Duke Street.
Flanagan has now been charged and will appear in court in the new year.
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A spokesperson 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.’
Flanagan is a graduate of Liverpool’s academy and played an integral role during the 2013/14 season when the Reds came close to winning the Premier League title.
However he’s struggled with injuries since then, with him failing to play the following season and spending time on loan at Burnley last term.
So far this season he’s made just one appearance, in the League Cup in September.
A Liverpool FC spokesperson 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.’
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