Cathay Pacific said the ICBM test didn't come close to the aircraft and it now has no plans to alter operations.
The flights, one from San Francisco and the other from Los Angeles, were both headed for Incheon, the main airport serving Seoul, South Korea.
The plane, which was flying from San Francisco to Hong Kong, was over Japan at the time.
The company told the BBC News Monday that a crew witnessed what was likely the reentry of the North Korean intercontinental ballistic missile (ICBM) into Earth's atmosphere last week.
He added that a separate Cathay Pacific flight, CX096, "might have been the closest [to the missile test], at a few hundred miles laterally", although there have been no reports from that flight's crew.
It should be noted though that if the latest test of the Hwasong-15 ICBM failed on re-entry, it did so on a lofted trajectory.
Cathay Pacific General Manager Mark Hoey sent a statement to the staff stating "today the crew of CX893 reported, 'Be advised, we witnessed the [North Korean] missile blow up and fall apart near our current location, '" according to the South China Morning Post.More news: Trump calls Roy Moore to offer his endorsement
Experts say the chance of a missile test hitting a civilian airliner is very low.
North Korea released an image of the November 29 launch of its most powerful ballistic missile yet.
"Though the flight was far from the event location, the crew advised Japan ATC (air traffic control) according to procedures".
But even some Trump advisers say United States military options are limited when Pyongyang could launch an artillery barrage on the South Korean capital Seoul - only around 50 kilometres (30 miles) from the heavily-fortified border and home to 10 million people.
"We have been in contact with relevant authorities and industry bodies as well as with other carriers".
Defense Secretary James Mattis said he still had confidence in diplomatic efforts to address the North Korea situation, but that the USA also has military options available. "We remain alert and (will) review the situation as it evolves".
Although airlines have not announced any moves to change routes following the most recent launch, Lufthansa, Swiss Airlines, and Scandinavian Airlines changed their routes in August following Pyongyang's first successful ICBM launches in July, the Financial Times wrote at the time.