The Archaeological Museum of Karpathos is housed in the west wing of the buildings of Eparheio. The exhibition is divided into three sections:
- Prehistoric times. It includes Neolithic findings from the Minoan / Mycenaean era.
- Historical times. In includes exhibits from the three ancient cities of the island: Karpathos, Arkeseis and Vroukounta.
- Byzantine times. It includes representative findings from the basilicas and villages of the island.