Barton's Turf return in doubt
The 34-year-old midfielder is alleged to have placed the bets between March 26th, 2006, when he was at Manchester City, and May 13th, 2016, less than a week after he had helped Burnley win the Championship title.
An FA statement said: "Joey Barton has been charged for misconduct in relation to betting.
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Hide Ad"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."
Only last month Barton was handed a one-match suspension by the Scottish Football Association after being found to have placed 44 bets between July 1st, when his Rangers contract officially started, until September 15th.
The midfielder still has that ban to serve, having had his contract with Rangers terminated by that point.
On Tuesday Burnley moved to end constant speculation over a return for Barton, with the player having accepted an offer to train at the club four weeks ago.
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Hide AdThey revealed a deal until the end of the season had been agreed, but whether that is now rubber-stamped remains to be seen.
Burnley released a brief 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."
Boss Sean Dyche had earlier spoken on Barton's proposed return, saying only: "He's not a contracted player at Burnley Football Club.
"We've just had a chat with him and agreed in principle the idea of it going forward."