Skymark is aiming to go head-to-head with Japan's two dominant carriers -- Japan Airlines (JAL) and All Nippon Airways (ANA) -- and stunned the industry last year when it ordered the A380s at a cost of $2.8 billion.
For Airbus, the deal gives the European firm a foothold in a market where US rival Boeing has long had a near-monopoly
"Skymark Airlines Inc. signed a firm contract with Airbus SAS for purchase of Airbus A380s on Thursday" in Toulouse, France, where Airbus is headquartered, the Japanese carrier said in a statement.
The airline ordered six A380s, including two on an optional basis, it said. The first aircraft is scheduled for delivery in 2014 and will be deployed on international routes.
The Japanese discount airline operator will use the six jetliners to operate its international passenger services linking Tokyo's Narita airport and three destinations, New York, London and Frankfurt, scheduled around the fiscal year ending March 2015.
If the services prove successful, Skymark plans to expand its service routes and will boost its A380 fleet.
Skymark, based at Tokyo's Haneda International Airport, has been operating since 1998 and currently offers domestic routes, offering lower fares than the two major Japanese carriers.
Skymark shares edged 0.07 per cent lower in Tokyo morning trade Friday.