The club's roots go back its founding on 8 September 1900, while more recently it has been linked with Sportverein Prussia Berlin and Pankower Fußball Verein Bergmann-Borsig.

[2] Weißenseer FC was part of the Märkischen Fußball-Bund, an early Berlin-based football league, where they captured the title in 1904.

Following World War II, Germany was occupied by the victorious Allies and the Weißensee district was part of the Soviet zone in Berlin.

It was standard practice in East Germany for clubs to have a sponsorship relationship with a local industry, service or government body as a Betriebssportgemeinschaft and in 1956 Blau-Weiß became BSG Einheit Weißensee.

In June 1993, the decision was made to join SV Preußen Berlin, a large sports club without a football department.

In 1997 Preußen folded its football team after its relegation from the Verbandsliga and re-founded Weißenseer FC which separated from the parent club after overcoming some legal difficulties.

Under the leadership of club president Ernst Konrad, it succeeded by bringing sponsors to pool their resources and hiring former DDR-Oberliga referee Reinhard Purzer as a coach.