A random test on July 5 showed the controller's blood-alcohol content was above the 0.02 percent maximum for on-duty controllers, the FAA said Tuesday.
The unidentified controller was six hours into an eight-hour shift at the Denver Air Route Traffic Control Center when the FAA tested employees for drugs and alcohol.
The Denver center oversees aircraft flying in several states.
The controller has since been removed from duty. Planes were not impacted by the incident.
The FAA said supervisors had no reason to suspect the controller had been drinking and that random tests are routine within the agency.
The Associated Press contributed to this story.