In 1943, Reichsmarschall Göring issued a request for design proposals to produce a bomber that was capable of carrying a 1,000 kg (2,200 lb) load over 1,000 km (620 mi) at 1,000 kph (620 mph); the so called "3 X 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 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 1.8x 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. A drogue parachute slowed the aircraft upon landing. The pilot sat on a primitive ejection seat. It was originally designed for the BMW 003 jet engine, but that engine was not quite ready and the Junkers Jumo 004 engine was substituted.