At the beginning of World War II, the Air Force of the Imperial Japanese Navy (IJN) had more aircraft than the IJA Air Force: about 1,750 fighters, torpedo bombers, and bombers, and 350 or more flying boats and float planes, used mainly for reconnaissance.

The organization of the naval air arm was complex, but its two major air units at the beginning of the war were the First Air Fleet, which operated aircraft carrier-launched airplanes, and the Eleventh Air Fleet, which operated land-based planes. Before the war was over, six more Air Fleets were formed: the Second, Third, Fifth, Tenth, Twelfth, and Thirteenth. Japan's Air Fleets were typically under the command of the commanders in chief of area naval fleets. Each Air Fleet was divided into at least two Air Flotillas, consisting of two or more Air Groups, each with 50 to 150 aircraft.

The naval air arm took the lead in aerial combat during the Pacific war. At the start of the war, its aircraft included some of the most advanced flown by any combatant, including the famed Zero fighter and the superb bombers, code named Nell, Betty, Jean, and Kate by the Allies. Admiral Yamamoto Isoroku was a strong believer in naval air power and saw to it that not only was the navy equipped with excellent aircraft, but that the planes were manned by highly skilled and thoroughly trained pilots. As the war progressed, however, Allied aircraft increasingly outclassed the Japanese, and pilot losses were so heavy that undertrained pilots were rushed into combat. A cardinal weakness of Japanese naval organization was its failure to use veteran pilots to train novices.

The naval air arm enjoyed early triumphs, most notably against Pearl Harbor on December 7, 1941. But the Battle of the Coral Sea, although a tactical air victory for Japan, resulted in a strategic defeat and heralded much worse defeat in the Battle of Midway, in which four Japanese aircraft carriers were sunk, many planes destroyed, and many experienced pilots killed. Midway forced Japan to assume the defensive for the rest of the war, which became a struggle of attrition that the Japanese could not sustain. Not only were they unable to make up their ongoing aircraft losses, but, even worse, they could not replace their best pilots. The worst aerial defeat of all came in the Battle of the Philippine Sea in June 1944, when 243 Japanese carrier aircraft were lost in what American pilots dubbed the "Great Marianas Turkey Shoot."

As the situation of the naval air arm became desperate, a desperate measure was formulated: the kamikaze, in which Japanese pilots deliberately used their aircraft as suicide weapons, human-guided missiles aimed at American ships.

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