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The F.IX was a three-engine, high-wing monoplane of conventional configuration, equipped with tailskid undercarriage. The wings were made of wood, and the fuselage was welded steel tube with a fabric covering. When presented at the 1930 Paris Air Show, it won the Grand Prix de Comfort et d'Elegance d'Avions de Transport - the "beauty prize" as voted by the public.

Czech aircraft manufacturer Avia purchased a licence to produce the type in order to create a bomber for the Czechoslovakian Air Force, when it was decided that the Fokker F.VII that Avia was already producing under licence was too small for this role. By 1932, 12 were in service as the F.39. Yugoslavia also purchased two aircraft, as well as a licence to produce the type domestically, although this did not eventuate. The F.39s differed from their civil counterparts not only in the addition of bomb racks, but also in a defensive machine gun being fitted to either a ventral "step" or a turret. Avia also built two examples as airliners for Czechoslovakian Airlines as the F.IX D (Dopravni - "transport"). One of these survived into World War II, when it was impressed into Luftwaffe service (as TF+BO).

Even though KLM directors had been talking in terms of ten or more aircraft in 1929, the worsening economic climate resulted in only two being purchased. Due to the logistics implications of stocking spares for only two aircraft, these were confined to European routes and the two F.IXs only ever made one flight each to the Indies. One (registration PH-AFK) was written off in a crash on 4 August 1931, and the other (De Adelaar, PH-AGA) was retired in 1936 and was subsequently acquired by clandestine means to serve as a bomber in the Spanish Republican Air Force during the civil war.