The name Folegandros is attributed by mythology to a son of the king of Crete, Minos, named Folegandros, considered the island's first settler; another version links the name to the Phoenician word for rocky, stony ground. Traces of habitation date back to prehistoric times, and the island's wild, fortress-like landscape shaped its fate from early on.
In antiquity Folegandros was inhabited by Dorians and later came under Athenian influence. Because of its isolation and rugged terrain, the Romans used it as a place of exile — a use that recurred in more recent times. At Chrysospilia, ancient inscriptions attest to cult activity as far back as classical times.
In Byzantine and medieval times the island suffered from pirate raids. After the Fourth Crusade, in 1207, it passed to the Venetians and was incorporated into the Duchy of the Aegean under Marco Sanudo; it was then that the settlement of the Kastro was fortified on the edge of the cliff, with its houses forming a continuous wall for protection.
In 1566 Folegandros passed to the Ottoman Empire, continuing to suffer pirate raids until the 18th century. It was incorporated into the Greek state after the Revolution of 1821, and in the 20th century it was again used as a place of exile. Thanks to the measured, gentle tourism of recent decades, the island has kept its authentic, tranquil character untouched.