Some flights were taking off over the ocean and in Alaska and Hawaii.
The Federal Aviation Administration ordered a rare nationwide ground stop Friday for all airports that lasted more than four hours.
Department of Homeland Security Secretary Markwayne Mullin told reporters it was due to a "telecommunications outage" and that there was no indication the incident was a "nefarious attack."
Nearly 5,000 flights were canceled amid the issue.
Homeland Security Secretary Markwayne Mullin reiterated that there was "no cyberattack" at the top of a press briefing Friday on the ground stop.
"I just want to reiterate this: The public was never at danger through this process. There was never any lives at risk. There was no flights at risk," he said.
The FAA said the nationwide ground stop is over, after more than four hours.
Transportation Secretary Sean Duffy and Homeland Security Secretary Markwayne Mullin will address reporters in the White House Briefing Room shortly regarding the FAA ground stop.
Amid the ground stop, United Airlines said it plans to cancel the majority of its remaining flights for the night, with exceptions for some international flights.
JetBlue said it is also canceling all remaining flights on Friday, save for Europe-bound flights departing from JFK and Boston.
"Flights already in the air are continuing to their destinations," JetBlue said in a statement. "We expect disruptions to continue into tomorrow, including additional cancellations."
Air Canada said it has canceled all remaining flights Friday between Canada and the U.S. due to the ground stop.
