[1][2] Two prototypes were created by attaching an extra pair of inner-wing segments to the wings of Ju 290 airframes and adding new sections to lengthen the fuselages.

It made its maiden flight on 20 October 1943 and performed well, resulting in an order in early 1944 for six more prototypes (Ju 390 V2 to V7) and 20 examples of the intended production version.

[3] The Ju 390 V1 was constructed and largely assembled at Junkers' plant at Dessau in Germany and the first test flight took place on 20 October 1943.

[3] The Ju 390 V1 was returned to Dessau in November 1944, where it was stripped of parts and finally destroyed in late April 1945 as the US Army approached.

At a hearing before British authorities on 26 September 1945, Professor Heinrich Hertel, chief designer and technical director of Junkers Aircraft & Motor Works, asserted the Ju 390 V2 had never been completed.

[8] German author Friedrich Georg claimed in his book that test pilot Oberleutnant Joachim Eisermann flew the Ju 390 V2 on 9 February 1945 at Rechlin air base.

[11] A speculative article in the British Daily Telegraph newspaper in 1969 titled "Lone Bomber Raid on New York Planned by Hitler", in which Hans Pancherz reportedly claimed to have made a test flight from Germany to Cape Town in early 1944.

A letter published in the 11 November 1955 issue of the British magazine RAF Flying Review (of which aviation writer William Green was an editor) claimed that two Ju 390s had made a flight to America, including a one-hour stay over New York City.

According to Green's reporting, in June 1944, Allied Intelligence had learned from prisoner interrogations that a Ju 390 had been delivered in January 1944 to Fernaufklärungsgruppe 5, based at Mont-de-Marsan near Bordeaux and that it had completed a 32-hour reconnaissance flight to within 19 km (12 mi) of the U.S. coast, north of New York City.

O'Donnell claimed that Albert Speer, in an early 1970s telephone interview, stated that there had been a secret Ju 390 flight to Japan "late in the war".