Early in 1943, a Junkers design team lead by Hans Wocke was assigned the task of developing a high-speed heavy bomber which could outrun any contemporary Allied fighter. They first looked at a turbojet-powered swept-back wing design. The swept-back wing offered advantages at the upper end of the performance envelope, but they were accompanied by disadvantages at low speeds. As a sweptback-winged aircraft slows down, its wingtip stalls first, causing a loss of roll control just when you need it the most. The Junkers team proposed a unique solution to this problem, a forward-swept wing. It was hoped that this wing would transfer the stability problems to the high-speed end of the performance envelope, where they could more easily be handled. In theory, the swept-forward wing would have its highest lift coefficient at the root, decreasing towards the tip. Consequently, the tip would be the last to stall as the aircraft slowed down, aileron control being available beyond the main centre-section flow breakaway.

The downside of the swept-forward wing design is in its elastic behaviour, specifically the phenomenon of "aero-elastic divergence". As an airplane flies through the air, its wing is subjected to a more-or-less random twisting moment exerted by variable aerodynamic forces caused by rapid changes in wind currents or by rapid manoeuvres. If the wing is swept forward, a small increase in the angle of attack at the tip will increase the lift, causing a twisting moment at the tip, which in turn will cause an increased angle of attack, which will cause still more lift, etc. This causes the aircraft to become seriously unstable. In the worst case, the wing can undergo a catastrophic structural failure. This can make for a real bad day.

The Reichsluftfahrtministerium (State Ministry of Aviation, better known as the RLM) gave the project the go-ahead and assigned it the designation Ju 287. The first prototype, the Ju 287 V1, was to be a flying testbed to check out the low-speed characteristics of the swept-forward wing. In order to get something in the air as soon as possible, parts were scavenged from existing aircraft to the extent feasible. The Ju 287 V1 used a fuselage from a He 177A bomber, a tail assembly from a Ju 388, and a massive fixed undercarriage consisting of Ju 352 mainwheels enclosed by large fairings and a pair of nosewheels scavenged from a B-24 Liberator. Virtually only the swept-forward wing was new. The wing used a Junkers reverse-camber, high speed airfoil section with a two-spar all-metal structure. The inner leading edges were fitted with fixed slats to delay the initial root stall, and large slotted flaps were fitted which extended down to 40 degrees. The ailerons were arranged to droop 23 degrees to provide a completely cambered wing for maximum lift coefficients. Power was provided by four 1984 lb. st. Junkers Jumo 004B turbojets, two mounted on the sides of the forward fuselage and two slung under the rear edges of the wings.

The Ju 287 V1 flew for the first time on August 16, 1944. Flight testing proceeded without any serious incidents, and the aircraft turned out to have rather pleasant flying characteristics. There were virtually no trim changes with flap operation, and landings were fairly easy. Lateral control was good except when yaw was applied, a pronounced wing drop then being experienced. The aircraft reached speeds as high as 404 mph in a dive, and confirmed the aero-elastic problems inherent in the swept-forward wing, with decreasing elevator forces during tight turns and pull outs from shallow dives.

Testing revealed that it would be a good idea to mount the engines on the forward edges of the wings in order to provide a mass balance, and this was to be done for the high-speed second prototype, the Ju 287 V2. The Ju 287 V3 was to be the production prototype with full military equipment being provided.

The wing of the Ju 287 V2 was similar to that of the V1, but the fuselage was entirely different, being quite similar to that of the propeller-driven Ju 388. A fully-retractable undercarriage was to be fitted, all members being stowed inside the fuselage. Originally, the plane was to be powered by four 2866 lb. st. Heinkel-Hirth 011A turbojets mounted in pairs and projecting ahead of the wing leading edges. However, owing to delays in the availability of this power plant, Junkers decided to power both the V2 and the V3 with six 1760 lb. st. BMW 003A-1 turbojets. Two different arrangements were to be tried, one with a cluster of three engines under each wing and the other with two engines underneath each wing and one on each side of the fuselage nose a la Ju 287 V1. The former engine arrangement was to power the V2, whereas the V3 and the pre-production Ju 287A-0 were to be powered by the second engine arrangement.

The V3 was to be the first prototype to carry armament: a tail barbette containing a pair of MG 131 machine guns operated remotely by a periscopic sight from the crew compartment. The cockpit was fully pressurized. A maximum bombload of 8800 lbs was envisaged. It was anticipated that the V3 could achieve a maximum speed of 509 mph at sea level and 537 mph at 16,400 feet. Range was expected to be 985 miles with an 8800 lb bombload. The V3 was expected to be able to attain an altitude of 19,700 feet in 10.5 minutes. Weights were estimated to be 26,278 lbs empty, and 47,398 lbs fully loaded.