The museum of Stutthof in Sztutowo was established as a result of an initiative of the Council for Commemoration of Struggle and Martyrdom and by a resolution passed by the District Council of Gdańsk on 12 March, 1962. Since 1 April, 1966 the museum has been directly subordinated to the Museum Department of the Ministry of Culture and Arts.

The idea to establish a camp for 'undesirable Polish elements' had originated among the Nazi authorities of the Free City of Gdańsk long before the war broke out. At least since 1936 officers of the Gdańsk police were observing and invigilating Polish circles, gathering materials which were used in 1939 as the basis to prepare lists of Poles to be arrested first. In July 1939 a special SS unit -'Wachsturmbann Eimann' was established. The main objective of that unit was, among others, to find locations and organize detention camps. In mid August 1939 the location of the future concentration Stutthof camp was selected.