The airline said the problem stems from air traffic control issues and weather.
"ATC issues and disruptive weather have resulted in a high volume of cancellations throughout the weekend while we work to recover our operation. We appreciate your patience as we accommodate affected Customers, and Customer Service wait times are longer than usual," the company said in a tweet Saturday.
ATC issues and disruptive weather have resulted in a high volume of cancellations throughout the weekend while we work to recover our operation. We appreciate your patience as we accommodate affected Customers, and Customer Service wait times are longer than usual. (1/2) pic.twitter.com/o1scQJ5lLb— Southwest Airlines (@SouthwestAir) October 9, 2021
The colossal travel hiccup comes in the midst of a busy time for airlines -- Monday is a federal holiday, meaning millions of American workers have a three-day weekend. More than 2.1 million people were screened at airport security checkpoints Friday, a volume that hasn't been seen since early August, according to the Transportation Security Administration.
Videos and images posted to social media show Southwest customers waiting in long lines that snake through airports in Denver, New York, Missouri and Arizona. Travelers in Chicago, Houston and other major U.S. city reported similar turmoil.
Current situation in Denver. Hundreds waiting for help with canceled @SouthwestAir flights. Every customer taking 30+ minutes to help. No support getting baggage and no support for hotels, etc. pic.twitter.com/eyJ0Bpsaif— Ryan Bevans (@Ryan_Bevans) October 10, 2021
The Federal Aviation Administration also told ABC News that it has attributed a few flight cancellations and delays on Friday to severe weather, military training and limited staffing at the Jacksonville Air Route Traffic Control Center.
"Some airlines continue to experience scheduling challenges due to aircraft and crews being out of place," an FAA spokesperson said in a statement.
Southwest pointed affected customers to its self-service rebooking options on southwest.com. The airline said it is working to recover operations and thanks customers for their patience.
MORE: Southwest employees must be fully vaccinated by Dec. 8 to keep jobs, company announces
Bad year for Southwest
Southwest has had a difficult year. The airline had the worst on-time performance and the greatest percentage of canceled flights of any of the nation's four major airlines in June and July, according to flight-tracking service Cirium.
Passengers aren't the only ones upset with Southwest: Unions for pilots, flight attendants and mechanics have all voiced complaints about the airline's operations.
Southwest promised to address the problems by scheduling fewer flights in the fall.
But Harteveltd noted Southwest's woes could linger and affect its fourth-quarter financial performance.
"All of this is happening as people are in the midst of booking their Thanksgiving and Christmas/New Year holiday travel," he said. "It's very possible that some people who might normally book on Southwest may see this news and choose to fly other airlines."
The Associated Press and CNN Wire contributed to this report.