Customers tweeted that they could not check in to flights on the No.4 U.S. airline by passenger traffic. Its reservations website, www.southwest.com, appeared to not allow booking or check-in and had a notice saying, "We're working hard to get you where you want to be... Thank you for your patience."
Southwest spokesman Dan Landson said a team is working to resolve the issues that began Wednesday afternoon following an outage. It will take time before the budget airline resumes a normal operation, he said.
Flight tracking website FlightAware.com showed that Southwest had delayed 157 flights so far on Wednesday, or about 3 percent of its operation.
Systems were gradually coming back online, Landson said. The airline tweeted at 4:55 p.m. Eastern (20:55 GMT) that "flight status and check-in are functional in our site waiting room." No further details were available.
The company's shares were down 1.6 percent at $42.03 at the closing bell.
The glitch follows several high-profile computer problems faced by U.S. airlines in recent months.
In October, a software failure at Southwest led to some 500 flight delays.
Industry consultants say the impact of computer disruptions will keep growing as airlines automate an increasing chunk of operations, distribute boarding passes on smartphones and outfit their planes with Wifi.