The move comes after the FA was criticised for punishing players for betting violations while having deals in place with gambling companies.
"At May's board meeting, it was agreed that The FA would end all sponsorships with betting companies starting from the end of the 2016-17 season," the FA said in a statement on Thursday.
"The decision was made following a three-month review of The FA's approach to it as a governing body taking betting sponsorship, whilst being responsible for the regulation of sports betting within the sport's rules.
"As a consequence, The FA has mutually agreed with Ladbrokes that its current partnership will be terminated from June 2017," concluded the statement.
FA rules ban players from betting on any football matches.
In April, former Manchester City and Burnley midfielder Joey Barton was banned for 18 months after he was found to have made more than 1,200 bets on football matches.
Barton, who said he had a gambling addiction, had pointed out the heavy involvement of the gambling industry in British football where bookmakers act as sponsors at several levels.
"That all means this is not an easy environment in which to try to stop gambling, or even to encourage people within the sport that betting is wrong," Barton had said in a statement.
England's second tier, run by the Football League, is known as the Sky Bet Championship, while numerous clubs have betting companies as shirt sponsors.
The FA said they would continue to work with betting companies, including Ladbrokes, in information sharing schemes on suspect betting patterns.
Martin Glenn, chief executive of The FA, said: "We would like to thank Ladbrokes for both being a valued partner over the last year and for their professionalism and understanding about our change of policy around gambling."
Jim Mullen, CEO of Ladbrokes Coral, said: "We understand The FA's decision regarding their commercial partnerships on gambling."
(Editing by John O'Brien)
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