The rise of Warnsdorf in 1939 was thanks to the annexation of the Sudetenland by Nazi Germany and the subsequent official abolition of professional football.

Warnsdorf brought players from dissolved or "deprofessionalised" teams, such as the two-time Czechoslovakia international Vilhelm Náhlovský from Teplitzer FK.

The success was immediate: in the 1938–39 season, Warnsdorf won the Gauliga Sudetenland with a 4–0 final win against Teplitzer FK and thus qualified for 1939 German football championship.

In 1940, the club did not return to the Gauliga Sudetenland and instead was absorbed by the new NSTG (National Socialist Gymnastics Community), and therefore could no longer build on previous successes.

Warnsdorfer FK's home stadium, the Platz am Hauptbahnhof, no longer exists and was replaced by a textile manufacturing facility.