Former England international Scholes, who spent his whole playing career at Premier League giants Manchester United, was a boyhood Oldham fan.
And the 44-year-old will now take charge of the League Two side, his first permanent role in senior management.
Scholes has long been linked with the Oldham job and emerged as the frontrunner for the post after the December sacking of Frankie Bunn.
A complication was Scholes' involvement in non-league Salford City, where he is a co-owner along with fellow former United stars David Beckham, Nicky Butt, Ryan Giggs, Phil Neville and Gary Neville.
But Scholes has now been cleared to take charge of Oldham and his first game in charge will come at home to Yeovil Town on Tuesday.