Scholes, who left League Two side Oldham Athletic a month into his first managerial post earlier this year, allegedly placed 140 bets on football matches.
The FA stated on Tuesday the bets were placed between August 17, 2015 and January 12, 2019 - prior to Scholes' appointment at Oldham.
He has until April 26 to respond to the misconduct charge.
Scholes, considered among the best midfielders of his generation, has previously taken temporary charge of non-league outfit Salford City, where he is involved in the ownership, in January 2015.
The United great is a part-owner of the club along with former team-mates David Beckham, Phil Neville, Ryan Giggs, Nicky Butt and Gary Neville.
Scholes, who made 66 international appearances for England, previously wrote a column for betting company Paddy Power.
In July 2017, the FA cut Joey Barton's ban from all football activity over betting breaches from 18 months to 13 months after the player appealed against the length of the sanction.
Barton, who did not play professionally again and is now in charge of Fleetwood Town, admitted placing 1,260 football-related bets between March 2006 and May 2016.
Omnisport have contacted Scholes' management for comment.