The archaeological findings indicate that Kimolos island has been inhabited at least since Neolithic times. According to tradition, the first settler was Kimolos, who gave it its name.

The island in ancient times was also known as Echinousa, probably because of the vipers ("echidnes") who lived (and still are) in the island. However, there is also another version, suggesting that the island might have gotten this name due to the many sea urchins.

During the 5th century BC Kimolos belonged to the Athenian League and became a battlefield during the Peloponnesian War. Actually, the ruins of the sunken city in Ellinika dates back to these ancient years. For the Roman and Byzantine era there is no particular information about Kimolos.

We do know that from 1207, when Marco Sanudo conquered the island, until 1537, Kimolos belonged to the Duchy of Naxos. At that time it was also called Arzantiera. However, in 1537 it was occupied by Barbarossa, and in 1638 it was greatly destroyed by pirates. This forced many people to leave Kimolos and find shelter in other places in the Cyclades (mainly Sifnos).

Generally raids were a massive scourge for the island, a scourge that residents tried to address by building the castle.

Kimolos participated in the Greek Revolution of 1821 and was one of the first to became part of the newly established Greek state.