Barton was given a one-match ban by the Scottish FA prior to leaving Rangers last month after admitting placing 44 bets between July 1 and September 15 this year.
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The 34-year-old trained with former club Burnley after making his Ibrox exit and is set to re-join the Clarets having agreed terms on a contract until the end of the season.
However, he could now face a longer ban if the fresh charges against him are proven.
An FA statement read: “Joey Barton has been charged for misconduct in relation to betting.
“It is alleged that between 26 March 2006 and 13 May 2016, he placed 1,260 bets on the result, progress, conduct or any other aspect of, or occurrence in, football matches or competitions in breach of FA Rule E8.
“He has until 5 January 2017 to respond to the charge.”
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Burnley issued a statement, saying: “Burnley Football Club have today been made aware of FA charges brought against Joey Barton relating to historic betting on football matches.
“The club will be discussing the matter with Joey and his legal representatives and will be making no further comment on the matter at this time.”
