Kea is the location of a bronze-aged settlement at the site now called Ayia Irini, which reached its height in the Late Minoan and Early Mycenaean eras (1600-1400 BCE).

In the Archaic period, the island was divided between four city-states (poleis): Ioulis, Karthaia, Poieessa and Koressos.

During the classical period, Kea (Ceos) was the home of Simonides and of his nephew Bacchylides, both ancient Greek lyric poets, of the Sophist Prodicus, and of the physician Erasistratus. The inhabitants were known for offering sacrifices to the Dog Star, Sirius and to Zeus to bring cooling breezes while awaiting for the reappearance of Sirius in summer; if the star rose clear, it would portend good fortune; if it was misty or faint, then it foretold (or emanated) pestilence. Coins retrieved from the island from the 3rd century BC feature dogs or stars with emanating rays, highlighting Sirius' importance.

During the Byzantine period, many churches were built and the prosperity of the island rose. It was Byzantine until, in 1204, it was captured by the Venetians in the wake of the Fourth Crusade. The Archbishop of Athens, Michael Choniates, came here in exile after his city fell to the Crusaders in 1205. It was recaptured by the Byzantines under Licario in 1278. In ca. 1302 during the Byzantine–Venetian War, it fell to the Venetians again, who built a castle on the ancient acropolis of Ioulis. In 1330 Cos became the seat of a Latin Church bishop but, since it is no longer a residential bishopric, it is today listed by the Catholic Church as a titular see. The earliest indication of it as a Greek bishopric is in a list by the Sicilian monk Nil Doxapatris of the second half of the 12th century and this may have been a later interpolation, since the list of the Greek bishops of Kea begins only at the end of the 16th century.

Kea was taken from the Venetians by the Ottoman Turks in 1537. Along with the rest of the Cyclades, Kea joined Greece following the Greek War of Independence in 1821.

HMHS Britannic, the largest ship sunk in World War I, which was the sister ship to the RMS Titanic and the RMS Olympic, sank off Kea island in 1916.