Scholes, 44, was appointed Oldham Athletic manager on a one-and-a-half-year contract in early February but has stepped down just over a month later.
“It’s is with great regret I have decided to leave the club with immediate effect. I hoped to at the very least, see out my initial term of 18 months as the manager,” Scholes said in a statement released to Press Association.
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The fans, players, my friends and family all knew how proud and excited I was to take this role.
“In short period since I took on role it unfortunately became clear I would not be able to operate as I intended and was led to believe prior to taking on the role.”
“I wish the fans, the players and the staff - who have been tremendous - all the best for the rest of the season and will continue to watch and support the club as a fan.”
The former Manchester United midfielder took charge of seven games, winning just one.
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