In order to improve performance, the Ju 388 was stripped of almost all defensive armament. Whereas the Ju 88 included a number of hand-swung guns in ports all over the cockpit area, on the Ju 388 they were replaced by a single remote-control turret in the tail containing two 13 mm (.51 in) MG 131 machine guns, aimed via a periscope in the cockpit, mounted one-above-the-other, as had been done experimentally with a few Heinkel He 177A heavy bombers' manned tail defensive gun positions. The Ju 388's remote tail turret had an excellent field of fire and could shoot directly to the rear, so the gunner's Bola streamlined casemate-style ventral defensive armament emplacement beneath the nose of Ju 88s and 188s was omitted, improving the aerodynamics.

The aircraft was to be delivered using the same naming as the three original Ju 188 experimental versions: the J, K, and L. The J model was a fighter with two 30 mm (1.18 in) MK 103 cannons and two 20 mm MG 151/20 cannons in a solid nose for use as a daytime bomber destroyer. For use as a night fighter, the long-barreled MK 103s were replaced by the smaller and lighter 30 mm MK 108s, while a second pair of dorsal-mount, upward firing MK 108s were added in a Schräge Musik installation behind the cockpit. The K model was a pure bomber, with a pannier under the plane increasing the size of the bomb bay. The L photo-reconnaissance model put its cameras in the pannier along with additional fuel tanks for long-range missions.

Three sub-models of each variant were planned, different only in the engine installation. The -1 would mount the 1,331 kW (1,810 PS) output BMW 801J, a turbocharged version of the basic BMW 801 air cooled radial, each engine installed as a unitized Triebwerksanlage engine installation format. The -2 would use the 46.4 litre displacement, 1,864 kW (2,500 hp) Jumo 222A/B 24-cylinder six-bank liquid-cooled engines, or the identical displacement 222E/F versions with an improved two-speed supercharger with triple intercoolers on each engine. The -3 would mount the Junkers Jumo 213E liquid cooled inverted V12, which included a supercharger similar to the 222E/F's. Since the 24-cylinder Jumo 222 engine was destined never to emerge beyond development and testing with just under 300 units ever built, the only powerplants actually used for the Ju 388 would be the BMW 801 radial and Jumo 213 series V12s.

With the BMW 801J or Jumo 213E, the fighter versions flew at 616 km/h (383 mph) when equipped as a destroyer, losing about 25 km/h (16 mph) to the eight-dipole Hirschgeweih antenna array used for late-war, VHF-band Neptun German AI radar and Schräge Musik when equipped as night fighters. This was similar in speed to existing Luftwaffe night fighters, but the Ju 388 maintained this speed at much higher altitudes. With the Jumo 222 engine, the aircraft was estimated to be capable of reaching around 700 km/h (435 mph), again losing about 25 km/h (16 mph) in night fighter versions. The bomber versions flew at roughly the same speeds depending on bombload, while the reconnaissance versions would have been about 25 km/h (16 mph) faster.

The first prototype, Ju 388 L-0/V7, mainly built from Ju 188 series production components, made its first flight on December 22, 1943. It demonstrated much better handling at altitude than the Ju 88S due to an increase in tail surface area, as the streamlined-nose Ju 88S, also omitting the Bola gondola, still used the original Ju 88A vertical tail surface design. This was followed by six new prototypes. It was some time before deliveries of the production models started due to engine delivery delays. By the time the engines were widely available, it was clear that B-29 bombers were being sent to the Pacific and would not be operating over Germany anytime soon. German photo-reconnaissance efforts had practically disappeared due to the increased performance of the Allied defenses, so production mostly concentrated on the L model.

Deliveries started in August 1944 but few Ju 388s were completed. About 47 L models seem to have been built, the majority as -1s with the BMW 801J engine, and just three -3s with the Jumo 213E. Fifteen K-1s were built; and only three J-1 models were produced.

Sources:
Gunston, Bill - The Encyclodepia of the Worlds Combat aircraft, 1976, Chartwell Books, Inc., New York
Brown, Eric, Captain - Wings of the Luftwaffe, 1979, Airlife Publishing Ltd., Shrewsbury
Gunston, Bill & Wood, Tony - Hitler's Luftwaffe, 1977, Salamander Books Ltd., London
Donald, David - The Complete Encyclopedia Of World Aircraft, 1997, Brown Packaging Books Ltd., London
Wikipedia - Junkers Ju 388