Rebuilding after the war proved difficult. The market was flooded with cheap surplus aeroplanes from the war. The company cautiously started building gliders and autobuses and converting Dakota transport planes to civilian versions. A few F25s were built. Nevertheless, the S-11 trainer was a success, being purchased by several air forces. The S-14 Machtrainer became one of the first jet trainers, and although not an export success, it served for over a decade with the Royal Netherlands Air Force.

A new factory was built next to Schiphol Airport near Amsterdam in 1951. A number of military planes were built there under license, among them the Gloster Meteor twin jet fighter and Lockheed's F-104 Starfighter. A second production and maintenance facility was established at Woensdrecht.

In 1958 the F-27 Friendship was introduced, Fokker's most successful post-war airliner. The Dutch government contributed 27 million guilders to its development. Powered by the Rolls-Royce Dart, it became the world's best selling turboprop airliner, reaching almost 800 units sold by 1986, including 206 under license by Fairchild. There is also a military version of the F-27, the F-27 Troopship.

In 1962, the F-27 was followed by the F-28 Fellowship. Until production stopped in 1987, a total of 241 were built in various versions. Both an F-27 and later an F-28 served with the Dutch Royal Flight, Prince Bernhard himself being a pilot.

In 1969, Fokker agreed to an alliance with Bremen-based Vereinigte Flugtechnische Werke under control of a transnational holding company. They collaborated on an unsuccessful regional jetliner, the VFW-614, of which only 19 were sold. This collaboration ended in early 1980.

Fokker was one of the main partners in the F-16 Fighting Falcon consortium (EPAF, European Participating Air Forces), which was responsible for the production of these fighters for the Belgian, Danish, Dutch, and Norwegian Air Forces. It consisted of companies and government agencies from these four countries and the United States. F-16s were assembled at Fokker and at SABCA in Belgium with parts from the five countries involved.

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