Brian Howard, 36, has been charged with one count of destruction of aircraft or aircraft facilities in connection with the fire in the building’s basement.
The man was found with burns and self-inflicted wounds. Investigators say Brian Howard used petrol to light the blaze.
By Friday afternoon flights in and out of O’Hare and Midway airports were slowly resuming.
More than 850 flights were cancelled in Chicago alone and many already in the air were redirected.
In a statement, the FBI said Brian Howard was charged on September but remained in hospital recovering from his injuries. No court date has been scheduled.
“We believe he set the fire and he used some kind of accelerant,” Aurora Police Chief Greg Thomas said in a news conference on September 26.
The building was damaged by the fire and the water used to extinguish the blaze.
Officials said they did not yet have a possible motive for the act but said Brian Howard was a contractor for the Federal Aviation Administration (FAA) and was authorized to be in the building. He had no ties to terrorism.
The fire broke out just before 06:00 local time on Friday morning in the Aurora, Illinois, air traffic control building, 40 miles west of Chicago.
Air traffic control officials said the radio frequencies with which they worked went dead and the control system was immediately shifted to a back-up system, the Chicago Tribune reported.
Workers used the back-up system until they were forced to evacuate.
“The [radio] frequency failed,” an unnamed controller told the newspaper.
“Depending on how bad the fire was, it could be a real mess getting things back to normal.”
One man was treated for smoke inhalation at the scene but no-one else was injured.
FAA spokeswoman Elizabeth Cory said management of the region’s airspace was transferred to another facility as the Aurora centre was evacuated.
By Friday afternoon, flights already on their way to Chicago were allowed to continue but landed at a slower pace.
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