Designed to supersede the D1A, the Aichi D3A became far better known than its predecessor. Of low-wing monoplane configuration, the prototype had elliptical wings similar to those of the Heinkel He 70, a conventional tail unit, and a circular-section fuselage. Construction was basically all-metal. Non-retractable tail wheel and landing gear incorporated main units with large speed fairings, and the prototype's engine was the 730 hp (544 kW) Hikari 1 radial that had powered the D1A2. Testing showed that the aircraft was under powered, had a tendency to snap roll in tight turns, and had ineffective dive brakes. The second prototype incorporated modifications to overcome these shortcomings, including increased wing span, changed outboard wing section leading edges to overcome the roll problem, strengthened dive brakes, and an 840 hp (626 kW) Mitsubishi Kinsei 3 radial engine. In this form the type proved superior to Nakajima's contender for this requirement, and in December 1939 was ordered into production under the designation Navy Type 99 Carrier Bomber Model 11 (Aichi D3A1).

Production aircraft differed from the second prototype by having a small decrease in wing span, and directional stability was improved by the addition of a long dorsal fin. Power was again increased, with the introduction of a 1,000 hp (746 kW) Mitsubishi Kinsei 43 engine on early production models. In this form the D3A1 completed carrier trials aboard the Kaga and Akagi, and entered operational service with the navy in China and Indochina. A total of 129 of these dive-bombers were carried by the task force that launched the attack on Pearl Harbor, and it was a force of D3A1s that sank the British aircraft carrier HMS Hermes, and the cruisers HMS Comwall and HMS Dorsetshire, in April 1942. At this time, the Aichi D3A enjoyed a bombing accuracy of 80 - 82 percent, and after releasing their bombs they were still effective dogfighters. This changed in late 1943, when the loss of skilled pilots saw the bombing accuracy drop below 10 percent, and this aircraft type ceased to be an effective threat.

Identified by the Allies under the code name 'Val', a total of 1,495 D3As of different versions were built. These included the two prototypes, plus six service trials and 470 D3A1 production aircraft. Then followed a single prototype of an improved D3A2 Model 12 which was first flown in June 1942. It differed by having a modified rear canopy, a 1,300 hp (969 kW) Mitsubishi Kinsei 54 radial engine, driving a propeller with spinner and increased fuel capacity to cater to the more powerful engine. Duly ordered as the D3A2 Model 22, this was the major production version, a total of 1,016 being built by Aichi (815) and Showa (201). With a maximum takeoff weight of 8,378 lbs (3800 kg), the D3A2 had a maximum speed of 267 mph (430 km/h) at 20,340 ft (6200 m) and service ceiling of 34,450 ft (10500 m). Final variant was the D3A2-K bomber trainer, of which an unspecified number of conversions were made from D3A2s late in the war, after the type had been relegated to second-line duties. With the appearance of the Yokosuka D4Y Suisei, the Aichi D3A was relegated to lesser important operations. Nevertheless, D3As remained in service from beginning to end of the Pacific war, serving finally in kamikaze roles. Nakajima developed a smaller version of this aircraft with retractable landing gear (D3N1), but the type was never adopted.