In 1954 was officially founded in Kimolos the local Archaeological Collection, thanks to the efforts of prominent citizens of the island to avert the transfer to the Athens National Archaeological Museum of numerous findings (more than 300 vessels), which came to light during excavations conducted by Nik. Kontoleon then Curator of Antiquities at the ancient city’s cemetery in the site “Hellenika”. To house the Archaeological collection, the foundation “Afentakeio” offered a small room at the nursing home of Kimolos.

Efforts to find a more suitable room for housing the ancient collection ended in 1970 when the Ministry of Culture accepted the donation of Eliza Vafia, who bequeathed the two-storey house of the doctor Vafias to install the Archaeological Museum of Kimolos.

Despite the continued efforts to repair the house, making it suitable for housing the museum, several years were spent until it became possible to begin the repairs of the building, which during that time had crumbled. Meanwhile, the ancient collection, had its numbers increased by the findings of the rescue excavations in the site “Hellenika”, but also from the surveys and the random finds. Therefore the collection-moved in 1994 to an area leased by the Ministry of Culture in the yard of Kimolos Nursing home, where a temporary, draft exhibition was created.

The work of restoration and conversion of the "Vafias house" to an Archaeological Museum (along with part of the next house expropriated for functional reasons) began in 1995 and was completed in 2001 with the responsibility and supervision of the Directorate of Technical Works Conduction in Museums, and then its function was administratively transferred to the KA’, (21st) Ephorate of Prehistoric and Classical Antiquities. In 2003 the collection moved to the restored building of the museum and the preparatory works for their permanent exhibition began ending the collections’ adventurous course. The task of organizing the areas of the museum and setting the permanent exhibition, was held under the project "Archaeological Museum of Kimolos", included in the Regional Operational Program 2000-2006 of the South Aegean with the Ministry of Culture and the KA’ (21st) Ephorate of Prehistoric and Classical Antiquities as implementing agencies. It was completed in 2005.

The Archaeological Museum of Kimolos opened to the public on July 11, 2006 and officially inaugurated on October 4, 2008.