Nearly 1,100 flights into and out of the two airports were canceled by 10:10 a.m. Central Time (11:10 am Eastern), according to tracking website flightaware.com, stranding thousands of passengers.
"There's cascading delays because nothing can take off bound for Chicago from anywhere,'' said Doug Church, spokesman for the National Air Traffic Controllers Association, a union of air traffic controllers. "The impact is national and major,'' he said.
At O'Hare, passengers were scrambling to find alternative transportation or bracing for long delays for flights to resume. "I'm shocked at how calm everyone is. With everything going on in the world, maybe we're all managing our expectations. It's a fire in Aurora, it's not ISIS,'' Cynthia Stemler of the Chicago suburb of Lake Bluff, who was heading to Newark, said, referring to militant Islamic group at war in Syria and Iraq.
O'Hare is the main hub for United Airlines and a major hub for American Airlines. From January to August, more than 580,000 flights departed or landed at O'Hare, the city of Chicago said, citing Federal Aviation Administration data.
"We anticipate a significant number of cancellations and delays throughout the day,'' United said in a statement.
Southwest Airlines Co suspended all flights until noon at Midway and Milwaukee's General Mitchell International Airport, the airline said in a statement. It was not clear what other airlines planned to do.
The FAA said employees were evacuated from its control center in Aurora when the fire broke out, reportedly at about 6 a.m. Central (1100 GMT).
"This has resulted in a ground stop for flights in the area and heading to Chicago,'' the FAA said in a statement.
Airspace management was transferred to adjacent air traffic facilities, it said. Crews responding to the fire found the man with knife wounds in the basement of the facility, who was then transported to a hospital, news reports said, citing the Aurora Police Department. Representatives for the police department could not be immediately reached for comment.
On May 13, about 700 flights were canceled at O'Hare and Midway airports after a faulty motor in the heating and cooling system at a flight control center in Elgin, Illinois, a Chicago suburb, caused smoke to circulate and forced staff to clear out of the building.
Flight operations at the Elgin center were transferred to the Aurora control center and limited arrivals and departures resumed more than three hours after the incident.