The bets cover a ten-year period dating back to when he was with Manchester City, his first senior club.
The FA confirmed on its Twitter feed: “Joey Barton has been charged for misconduct in relation to betting.”
The former Rangers midfielder is now facing another suspension after already being found guilty of breaking betting rules in Scotland.
Barton was handed a one-match ban by the Scottish Football Association last month.
He has yet to serve the suspension because he is currently without a club having had his Ibrox contract terminated.
He has been training with Burnley and will join his former club when the transfer window opens in January.
The SFA found Barton, 34, guilty of placing 44 bets on games between 1 July, when his Rangers deal started, until 15 September. His suspension will be carried over when he signs for Burnley.