A number of archaeological findings were collected in 1925 in two rooms inside the madrasa of Sultan Bayazid II Kulliye, which, together with the mummies from the Ilkhanate, were initially placed in a museum warehouse. As the number of items to be displayed grew, it became evident that new locations were needed. Thus, all the items were moved in 1962 to the Gökmedrese Mosque, a building that dates back to the Seljuk Era.
The museum moved to its current modern building on 22 March 1977. Following a detailed work for rearrangement, all items were classified according to a chronology-based listing and the museum officially opened in 1980.
The Archaeological Museum of Amasya consists of three sections: the Hall of Archaeological Artifacts, where items from 13 civilizations are on display; the Hall of Ethnographical Artifacts, where items from regional handicrafts and life culture are on display; and the Hall of Mummies inside the Sultan Mesud I Tomb in the museum yard, where mummies from the Ilkhanate period are displayed.
Amasya Museum consists of Şehzadeler Museum, Milli Mücadele Museum, and Hazeranlar Konağı Museum.