The Federal Aviation Administration on Sunday said all Delta Air Lines Inc's domestic flights were grounded until 0100 GMT after a request from the company due to an "automation issue."
The problem affects all Delta mainline and sub carriers to domestic destinations, but international flights are exempt, the FAA said in an advisory.
"Delta teams are expeditiously working to fix a systems outage that has resulted in departure delays for flights on the ground," the company said in a statement.
"Flights in the air remain unaffected. Delta apologizes to customers for the inconvenience."
Several passengers took to Twitter to express their dismay, with some saying they had to wait for hours before being told of the problem.
Airports across the country were thrown into chaos after President Donald Trump on Friday put a four-month hold on allowing refugees into the United States and temporarily barred travelers from Syria and six other Muslim-majority countries, saying the moves would help protect Americans from terrorist attacks.
Confusion abounded at airports as immigration and customs officials struggled to interpret the new rules, with some legal residents who were in the air when the order was issued detained at airports upon arrival.
Just last week, United Airlines said it had grounded all domestic flights due to an "IT issue."
(Reporting by Devika Krishna Kumar in New York; Editing by Lisa Von Ahn)