The 40 airports selected by the FAA span more than two dozen states and include hubs like Atlanta, Dallas, Denver, Charlotte, North Carolina, and Los Angeles.
A closer look at FAA order's impact on California
No state will feel the impact more than California.
San Diego International Airport (SAN), OAK Oakland International Airport (OAK) and SFO San Francisco International Airport (SFO) also made the list, bringing the total number of California airports impacted to five.
At around 11 a.m. on Friday, there were 53 flights in and out of LAX that were canceled. At Ontario International Airport, there were only eight canceled flights.
While Hollywood Burbank Airport isn't on the list of affected airports, there were still 14 cancellations reported.
"United said coming back into L.A., they're going to try to keep a lot of the flights open ... keeping my fingers crossed that happens," said one traveler who spoke with Eyewitness News on Friday.
Why is this necessary?
Air traffic controllers have gone without paychecks during the shutdown. That has led to controllers calling in sick and contributed to staffing shortages that have affected air travel for weeks.
Most controllers work mandatory overtime six days a week during the shutdown without pay, the National Air Traffic Controllers Association has said.
When will the reductions begin and end?
Airlines will phase in reductions at the direction of the FAA, starting by eliminating 4% of flights at the targeted airports and building to 10%, according to the agency's order.
United Airlines will cut 4% of its flights this weekend based on guidance from the FAA, said company spokesperson Josh Freed.
What will the effect of the reduction be?
The cuts could include up to 1,800 flights and about 268,000 seats combined, according to one estimate.
United and Delta both said they would offer refunds to travelers who opt not to fly, even if they have tickets that aren't normally refundable.
The cuts also could disrupt package deliveries because two airports with major distribution centers are on the list. FedEx operates at the Memphis, Tennessee, airport and UPS in Louisville, Kentucky, where there was a deadly cargo plane crash this week.
The pain was lessened a bit Friday for some flying United and American as both airlines said they were able to quickly rebook most of their travelers affected by the cuts.
The vast majority of the more than 80% rebooked by United Airlines have been scheduled to reach their destinations within four hours of their original plan, a spokesperson said Friday.
What do I do if my flight is canceled?
Airlines directed passengers with weekend travel plans to check their apps to get the latest on their flight status.
Carriers are required to refund customers whose flights are canceled but not to cover secondary costs such as food and hotel accommodations unless a delay or cancellation results from a contributing factor that is within the control of the airlines, according to the Department of Transportation.
Industry analyst Henry Harteveldt warned that the reductions will "have a noticeable impact across the U.S. air transportation system."
The cuts could also slow package service as two airports on the list are major distribution centers for delivery companies: FedEx in Memphis, Tennessee, and UPS in Louisville, Kentucky, the site of this week's deadly cargo plane crash.
The Associated Press contributed to this report.