Cathay Pacific flight CX893 was making its way over Japan when Pyongyang fired the Hwasong-15 intercontinental ballistic missile.
Those on board reported seeing what they thought to be the missile re-entering the atmosphere.
After last week's launch, the rogue state boasted that the weapon was capable of hitting the US mainland.
A spokesman for the airline told Sky News: "On 29 November, the flight crew of CX893 reported a sighting of what is suspected to be the re-entry of the recent DPRK test missile.
"Though the flight was far from the event location, the crew advised Japan ATC (air traffic control) according to procedures. Operation remained normal and was not affected.
"We have been in contact with relevant authorities and industry bodies as well as with other carriers. At the moment, no one is changing any routes or operating parameters. We remain alert and review the situation as it evolves."
The South China Morning Post reports that the airline's general manager of operations Mark Hoey posted on the internal company communications platform to warn colleagues of the flight's proximity to the missile.
He said the crew had witnessed the missile "blow up and fall apart near our location" and that another Cathay Pacific flight - CX096 between Hong Kong and Anchorage in Alaska - may have been even closer.
Tensions in the region are likely to escalate even further this week, with North Korea declaring a five-day joint military drill between the US and South Korea as an "open, all-out provocation".
The two allies began their largest ever co-operative air exercise - dubbed Vigilant Ace - on Monday, with 230 aircraft, including 24 stealth fighter jets, set to take part.