In June 1937, The Imperial Japanese Navy issued a specification to the Aichi, Nakajima, and Kawanishi companies calling for a two-seat reconnaissance floatplane of monoplane configuration to replace the aging Kawanishi E7K2 three-seat twin-float seaplane. The three manufacturers responded with three prototype designs designated E12A, E12N, and E12K, respectively. But even as these three designs were being created, a new specification was issued calling for a larger, three-seat monoplane reconnaissance seaplane, with higher speed and longer range for convoy escort duty. Three additional designs were created by the engineering teams of the companies involved, intending to compliment rather than replace earlier designs. These were designated Aichi E13A, Nakajima E13N, and Kawanishi E13K. Aichi was the only one to build both of its designs with Nakajima deciding to concentrate on the two-seat version while Kawanishi concentrated on the three-seat version.
Kishiro Matsuo's design team created both the E12A and the E13A, the latter being merely a larger and more powerful version of the former. The first E13A was completed in late 1938 add powered by a 1,080 hp (805 kW) Mitsubishi Kinsei 43 14-cylinder air-cooled radial (which was retained throughout the life of the type). During manufacturer's test flights, it became plain that the E13A was superior to the smaller E12A. Not withstanding its larger size and heavier weight, it was much more stable and manoeuvrable, and also had far better performance. By this time, the Navy had decided they wanted a three-seat aircraft and not a two-seater, so development of the two-seat E12A and E12N was halted. Service test pilots flew the prototype E13A in competition against two prototype E13Ks built by Kawanishi. In December 1940, the E13A was formally declared the winner and was accepted for production as the Navy Type 0 Reconnaissance Seaplane Model 11, or E13A1 Model 11. Aichi built 133 E13A1s through early 1942, when they were ordered to concentrate on building the Yokosuka-designed D4Y carrier dive bomber and recon plane. At that time, primary builder of the E13A became the Watanabe Tekkosho (Watanabe Ironworks Company Limited) which in 1943 was re-organized as Kyushu Hikoki KK (Kyushu Airplane Company Limited). Total aircraft production was 1,418 aircraft. Aichi Tokei Denki KK building 133 aircraft from 1939-42, Watanabe/Kyushu building 1,237 aircraft from 1942-45 and Dai-Juichi Kaigun Kokusho (11th Naval Air Arsenal) building 48 aircraft from 1940-42.
The Aichi E13A1 made its combat debut over China in the autumn of 1941. Operating from the catapults of cruisers and seaplane tenders, aircraft of this type made air attacks on the Canton-Hankow Railroad, and also flew anti-shipping patrols along the China coast. Its next combat sorties were flown over Hawaii, launched from the cruisers Tone, Chikuma, and Kinugasa. Aichi E13A1s flew reconnaissance over the area of Pearl Harbour shortly before the attack, pinpointing the positions of the American ships in the harbour and noting that all was quiet, and the Americans were not on alert. From then on, E13A1s were committed wherever the Japanese Navy was operating. Flying from either ships or shore bases, as required, the E13A1 was quite successful as long as Allied fighter opposition was limited, despite its poor fuel and crew protection and its pitiful defensive armament (a single 7.7 mm (0.303 in) machine gun in the rear cockpit). It could carry either one 551 lbs (250 kg) bomb under the fuselage between the floats, or four wing-mounted 132 lbs (60 kg) bombs or depth charges. Its maximum endurance was almost fifteen hours, giving it a useful range for patrol and reconnaissance missions. In addition to limited bombing strikes and long-range patrol sorties, the "Jake" as she was code-named, also was used for staff transport, air-sea rescue, anti-shipping attack, and, later in the war Kamikaze attacks.
For nearly four years, the Jake was built without any changes from the original prototype. In November 1944, two new subtypes were introduced, differing externally from the regular E13A1 only by the additions of a propeller spinner for the three-bladed propeller, and two extra pairs of inward-sloping bracing struts for the twin underwing floats. The E13A1a Model 11A received improved radio equipment, while the E13A1b Model 11B was fitted with an air-to-surface search radar, with antennae protruding from the fuselage sides and from the wing leading edges. Either of these versions could be fitted with exhaust flame dampers for night operations, and for anti-shipping attack (usually against surfaced submarines or PT boats), a single flexible Type 99 20 mm cannon, firing downwards and forwards from the fuselage belly, could be mounted, as well. Some Jakes were also fitted with an aerial magnetic submarine detection device, called Jikitanchiki, which required the aircraft to fly at a very low 30-40 ft (9-12 m) above the sea's surface to get any decent results.
Due to the theatre the Japanese operated in and the vast expanses of ocean it encompassed, long range seaplanes were crucial to the Japanese war effort. The Aichi E13A served from Pearl harbour to some of the last Kamikaze attacks of the war. Although easy fodder for Allied fighters the Aichi E13A and its crews performed their missions well throughout the Pacific War.