Alaska Airlines said it had ended the ground stop, which lasted about three hours and resulted from a software outage. “Residual impacts” to its operations were likely, it said.

Alaska Airlines resumed operations early Monday after grounding its entire fleet of planes and those of a subsidiary because of a software outage for about three hours.

The airline first requested to ground the more than 200 aircraft it operates under the Alaska Airlines brand at about 11 p.m. Eastern time, according to an advisory released by the Federal Aviation Administration. The ground stop was then expanded to include planes from Horizon Air, a unit of Alaska Airlines.

The airline said at about 2 a.m. on Monday that the ground stop had been lifted and its operations had resumed.

“As we reposition our aircraft and crews, there will most likely be residual impacts to our flights. It will take some time to get our overall operations back to normal,” it said on social media.

Alaska Airlines said in late April that it was operating 238 planes, all Boeings, under its brand, and another 45 planes under the Horizon Air brand.

Alaska Airlines is the fifth largest U.S. airline, according to its website. It flies to more than 120 destinations in five countries and has more than 44 million customers each year.

Several passengers reported being stalled on the tarmac for more than an hour as they awaited information from airline staff, and before finally being ferried off their flights. Late on Sunday evening, some were still waiting to be reunited with their luggage, or placed on alternative flights. Others said they had yet to get off the plane.

Grant Watts, a passenger on an Alaska Airlines flight grounded at Denver International Airport on Sunday night, said that he and his fiancé had been waiting on the tarmac for two hours. At about 10:30 p.m., passengers were finally informed that they would have to exit the plane, Mr. Watts said.

The F.A.A. did not immediately respond to a request for comment.