The 48-year-old, who recently guided the nation to World Cup qualifying wins over San Marino and Czech Republic, was detained by police in Scotland.
According to The Mirror, O'Neill was pulled over at around 12.55am on Sunday just outside of Edinburgh, and was later charged.
A statement from the Irish FA read: "[We are] aware of an alleged drink-driving incident involving Michael O'Neill. As it is a police matter, the Association will be making no further comment."
The former Shamrock Rovers boss is due to appear in court on October 10, which is two days after the Green and White Army face Norway in a qualifier.
The team are guaranteed a playoff spot as they currently sit second in Group C.