In the early 1930s, the Horten brothers had become interested in the flying wing design as a method of improving the performance of gliders. The German government was funding glider clubs at the time because production of military and even motorized aircraft was forbidden by the Treaty of Versailles after World War I. The flying wing layout removed any "unneeded" surfaces and theoretically offered the lowest possible weight, using wings that were relatively short and sturdy, and without the added drag of the fuselage. The result was the Horten H.IV.

In 1943, Reichsmarschall Göring issued a request for design proposals to produce a bomber that was capable of carrying a 1,000 kilograms (2,200 lb) load over 1,000 kilometres (620 mi) at 1,000 kilometres per hour (620 mph); the so-called "3×1000 project". Conventional German bombers could reach Allied command centers in Great Britain, but were suffering devastating losses from Allied fighters. At the time, there was no way to meet these goals—the new Junkers Jumo 004B turbojets could provide the required speed, but had excessive fuel consumption.

The Hortens concluded that the low-drag flying wing design could meet all of the goals: by reducing the drag, cruise power could be lowered to the point where the range requirement could be met. They put forward their private project, the H.IX, as the basis for the bomber. The Government Air Ministry (Reichsluftfahrtministerium) approved the Horten proposal, but ordered the addition of two 30 mm cannons, as they felt the aircraft would also be useful as a fighter due to its estimated top speed being significantly higher than that of any Allied aircraft.

The H.IX was of mixed construction, with the center pod made from welded steel tubing and wing spars built from wood. The wings were made from two thin, carbon-impregnated plywood panels glued together with a charcoal and sawdust mixture. The wing had a single main spar, penetrated by the jet engine inlets, and a secondary spar used for attaching the elevons. It was designed with a 7g load factor and a 1.8× safety rating; therefore, the aircraft had a 12.6g ultimate load rating. The wing's chord/thickness ratio ranged from 15% at the root to 8% at the wingtips. The aircraft utilized retractable tricycle landing gear, with the nosegear on the first two prototypes sourced from a He 177's tailwheel system, with the third prototype using an He 177A main gear wheelrim and tire on its custom-designed nosegear strutwork and wheel fork. A drogue parachute slowed the aircraft upon landing. The pilot sat on a primitive ejection seat. A special pressure suit was developed by Dräger. The aircraft was originally designed for the BMW 003 jet engine, but that engine was not quite ready, and the Junkers Jumo 004 engine was substituted.

Control was achieved with elevons and spoilers. The control system included both long-span (inboard) and short-span (outboard) spoilers, with the smaller outboard spoilers activated first. This system gave a smoother and more graceful control of yaw than would a single-spoiler system.