The Phoenician word "phelekgundari" means rocky land and is one of the possible roots of Folegandros's name. By another account, the island is named after its first inhabitant, Folegandros, a son of the King Minos of Crete. Under Venetian rule, the island's official name became "Polykandros".
After the fall of Constantinople in 1204 and the emergence of Venice as the supreme power in the Aegean, Venetians and Turks sought to seize control of the island.
In 1715, Folegandros fell to the Turks. It was united with Greece in 1828.
During the Metaxas dictatorship, Folegandros became a place of internal exile, much as it had been during Roman rule.