Halki's history is intertwined with Rhodes. The few data available indicate that Halki was slave to Kameiros for long periods, following its rise and fall as well as Rhodes'.

In the 14th century the Knights who control Rhodes and the surrounding area grant Halki as a fief to the Assanti family. At that time, the castle of the island was constructed upon the ruins of the ancient acropolis. The castle was used as a shelter by the islands' inhabitants during the several attacks by pirates and others.

The early 16th century finds Halki, together with the rest of the region, under Ottoman occupation, enjoying many privileges that allow it to survive through commerce. Yet, following the example of islands like Kalymnos and Symi, Halki owes its great economic and intellectual prosperity to sponge fishing.

Although it participates in the Greek revolution in 1821, it remains under Turkish control until 1912 when Italians occupy the island. In 1948 Halki, together with the other Dodecanese, is finally liberated and becomes an integral part of Greece.