The 'BBC' are reporting that Fry allegedly placed bets on matches or competitions during the 2017-18 season, in breach of FA rules.
Fry, 73, has until December 20 to respond to the charges.
Fry is a former manager of English Football League clubs including Birmingham City, Southend United and 'The Posh', who are fourth in League One.
A statement from Peterborough said: "The football club are working closely with the FA on this matter. The club will make no further comment at this time."