The decision was taken after Seattle District Judge James Robart announced a temporary suspension of US President Donald Trump's week-old executive order temporarily barring refugees and nationals from seven countries from entering the US.
Spokespersons for Qatar Airways and US-based United Airlines confirmed to Al Jazeera that they will board all passengers with valid travel documents that are affected by the order after receiving an advisory to do so from the CBP.
"As directed by the US Customs and Border Protection, nationals of the seven affected countries listed below and all refugees seeking admission presenting a valid, unexpired US visa or [green card] will be permitted to travel to the United States and will be processed accordingly upon arrival," read a travel alert posted on Qatar Airways' website.
The judge's temporary restraining order represents a major challenge to Trump's action, although his administration could still appeal the ruling and have the policy upheld.
It comes on the heals of a week's worth of spontaneous protests at airports across the country.
The US state department said it is working with the Department of Homeland Security to work out how Friday's ruling affects its operations, and will announce any changes affecting travelers as soon as information is available.
The White House said it would file an appeal as soon as possible.
"At the earliest possible time, the Department of Justice intends to file an emergency stay of this outrageous order and defend the executive order of the president, which we believe is lawful and appropriate," the White House said in a statement. A revised statement released later omitted the word "outrageous".
"The president's order is intended to protect the homeland and he has the constitutional authority and responsibility to protect the American people," the White House said.
Trump's executive order bars Syrian refugees indefinitely and blocks citizens of Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen entry into the US for 90 days. Refugees from countries other than Syria are barred from entry for 120 days.
The state department said on Friday that up to 60,000 foreigners from the seven countries concerned had their visas cancelled as a result of the order. A justice department attorney, however, told a court hearing in Virginia that about 100,000 visas had been revoked.
The ban caught the airline industry off guard, with some carriers forced to re-roster flight crew in order to abide by the order.