What is now the museum building was originally a school - the first one on the island. In the periods when Ai-Stratis was a place of exile for political internees it was used as an infirmary. The building was so badly damaged by the 1968 earthquake that it had to be abandoned. In 2005 restoration work was put in hand by the Ministry of Culture (Department of Modern Monuments and Engineering Works, North Aegean Region). The restoration was completed in November 2007.
The task of collecting the exhibits and organizing the museum was undertaken by the Ministry of Culture's Directorate of Modern Cultural Heritage.