The Navy ordered two prototypes and plans were submitted by Nakajima and Mitsubishi. Nakajima elected to drop their proposal for a fighter design and Mitsubishi submitted their design led by designer Jiro Horikoshi. The Mitsubishi prototype was the A6M1, retractable gear, all metal, low-wing monoplane, powered with a 780 hp Mitsubishi Zuisei 13 engine. During flight testing, the two-bladed prop variable-pitch propeller was replaced with a three-bladed variable pitch propeller. Apart from maximum speed, all requirements were met or exceeded. The Navy had authorized the production of an initial batch of A6M2s and military trials progressed rapidly. While flight testing the A6M1, a new power plant passed its Navy acceptance tests, and the 925 hp Nakajima NK1C Sakae 12, which was slightly larger than the Zuisei, was installed in the third A6M2 prototype. The initial trials were completed in July 1940 and the navy assigned fifteen A6M2s to combat trials in China. In China the A6M2s, reinforced with a number of production aircraft, destroyed 99 Chinese aircraft with a loss of only two of their own. The aircraft was accepted for production on July 1940 as Navy Type 0 Carrier Fighter Model 11 and in September 1941 were prepared for the impending war with the Allies. Modifications were introduced during production and A6M2 rear spar was reinforced and manually folding wingtips were incorporated to allow clearance on the carriers deck elevators. The modified aircraft was designated Navy Type 0 Carrier Fighter Model 21. The A6M2 Model 21 was the version utilized at Pearl Harbour and throughout the Pacific, during the early stages of the war. With its maximum speed of 288 kt @ 4,550 m and ability to climb to 6,000 m in 7 minutes 27 seconds, it possessed an ascendancy over any other fighter type in the Pacific. When the war began on December 7, 1941, the Japanese Navy had 328 A6M2s in first line units.

The A6M possessed many shortcomings, which were only to be revealed six months later when a virtually intact specimen was obtained. On June 3, 1942, Flight Petty Officer Tadayoshi Koga left the flight deck of the carrier Ryujo in his Mitsubishi A6M2 Model 21 fighter as part of a task force assigned to attack Dutch Harbour in the Aleutian Islands. His A6M2, which had been built in February, was on its first operational mission. On his way back to the Ryujo, Koga found that two bullets had punctured his fuel supply and he informed his flight commander that he intended to land on Akutan Island, designated as an emergency landing field. Koga did not make the landing field and instead made a forced landing in a marsh where the aircraft flipped over, in which he was killed, from a broken neck. Five weeks later, a US Navy PBY Catalina, making a routine patrol, discovered the Japanese fighter upside down in the marsh. This single fighter was probably one of the greatest prizes of the Pacific war. Hardly damaged, it was shipped back to the USA where it was exhaustively tested. Information gathered during testing of the A6M2 prompted the American aircraft manufacturer Grumman, to lighten the Grumman F4F Hellcat, and install a larger engine on the Grumman F6F Hellcat.

Some Zeros were the first aircraft used intentionally as suicide attack planes. Modified Zeros assigned to Air Group 201 in the Philippines became the first Japanese aircraft used on planned suicide missions against American surface vessels. Air Group 201, assisted by volunteer pilots from Air Group 601 and other Navy units in the area, became the first Kamikaze (Divine Wind) suicide squadron in the Japanese Naval Air Force. The outstanding successes gained by this form of attack led to the formation of other Kamikaze units, and the bomb-carrying Zeros became the prime suicide attack bombers of the Navy.