The former Red Devils midfielder is alleged to have placed multiple bets on football in contravention of FA regulations
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, 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.
Scholes, considered among the best midfielders of his generation, is a Manchester United legend having made more than 700 appearances for the club between 1993 and 2013.
He initially retired from playing in 2011 but reversed that decision the following year to help the club through an injury crisis.
The midfielder ultimately agreed a new deal through the end of the 2012-13 season, helping the team to the Premier League title – the 11th league winners’ medal of his career.
After retiring for a second time Scholes began his coaching career with Manchester United Under-19s in an informal basis alongside Nicky Butt. He also joined the first-team coaching staff on a temporary basis when Ryan Giggs was appointed interim manager at the end of the 2013-14 season.
The same year Scholes joined with former team-mates and fellow members of the ‘Class of ‘92’Giggs, Butt, David Beckham, Phil Neville and Gary Neville in buying non-league side Salford City.
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In January 2015 Scholes and Phil Neville took temporary charge of Salford for a game against Kendal Town following the sacking of manager Phil Power.
He was appointed manager of Oldham in January of this year, his first full-time managerial position.
He would only be in charge for seven matches, winning one, before resigning, saying he was unable to “operate as intended” and has stated he was misled before taking the job.