The Archaeological Museum of Naxos is housed in a historic five-storey building, constructed in the 17th century to house the School of the Jesuits of the island. The building developed along the Frankish castle, incorporating two of the towers of the castle. In late 19th century the building was the seat of the well known Commercial School of Naxos, among the students of which was the famous Greek author Nicos Kazantzakis. Later on, the building was allotted to the Archaeological Service of Greece and since 1973 it houses the Archaeological Museum of the island.

Numerous exhibits are very important and come from the excavations carried out on the island the last 60 years. The finds displayed cover a period of more than 6000 years, from the Neolithic Period up to the Early Christian era. Of course, the most outstanding among them is the collection of Cycladic statuettes of marble, dated in the Early Cycladic period (3200 -2300 b.C.). The collection of the Museum for this period of history is considered by specialists of equal importance and archaeological and artistic value with those housed in Athens, in the National Archaeological Museum and in the Museum of Cycladic Art. Apart from the Early Cycladic collection, the Museum has also rich collections of typical vessels of the Mycenaean period and of Geometric times (9th and 8th century b.C).