The computer systems were back up and running by Friday afternoon, as authorities scrambled to process the backlog of waiting travelers.
At LAX, arriving international travelers were stuck for hours as they waited to enter the country
"This is ridiculous," said Lani Byhoffer, a traveler returning from Budapest. "I'm ashamed for America. I am ashamed. We waited in line for almost two hours today. Somebody can come up with a better system than what we went through today."
Anyone arriving to LAX to pick up international travelers should expect delays.
The outage affected major airports throughout the country, including John F. Kennedy Airport in New York, Bush Intercontinental Airport in Houston, O'Hare and Midway airports in Chicago, San Francisco International Airport, and Philadelphia International Airport.
A government official told ABC News that there's no indication that Friday's interruption was a malicious attack on the network "at this time."
Passengers in many airports were being processed manually, so travelers throughout the United States should expect longer than normal wait times.
The outage only impacted airports, according to a CBP official, not other ports of entry like seaports or land border crossings. The outage did not impact flight departures.
"CBP officers are working to process travelers as quickly as possible while maintaining the highest levels of security," a spokesperson said in a statement.
An American Airlines spokesperson tells ABC News they were "aware" of the outage and in contact with U.S. Customs and Border Protection.
A picture posted to Twitter by Sarah Baird showed massive crowding in the customs line.
"This is I'm in the global entry line and the regular line has several hundred if not thousands in it," she tweeted.