Iraklia has been inhabited since deep antiquity and always belonged to the sphere of influence of neighboring Naxos. Its name is attributed to the hero Heracles, while the ruins of the Hellenistic tower above Livadi attest to organized habitation and fortification already from ancient times. The Cave of Ai-Giannis appears to have been known and used for worship since ancient times.
During Roman and Byzantine times the island followed the fate of the surrounding Cyclades. After the Fourth Crusade and the fall of Constantinople (1204), Iraklia was incorporated into the Venetian Duchy of the Aegean, based in Naxos.
During the years of piracy, like most small Aegean islands, Iraklia was almost completely deserted: the inhabitants abandoned the coasts to escape the raids. For long periods the island remained uninhabited, used only for grazing and cultivation by residents of Naxos and Amorgos.
Permanent resettlement came in the 19th century, when families mainly from Amorgos and Naxos settled on the island, living from livestock farming, agriculture and fishing. Today Iraklia, with very few permanent residents, remains one of the most untouched and authentic islands of all the Cyclades.