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Kochi owes its existence to a flood. In 1341 the Periyar burst its banks, silting up the ancient harbour of Muziris to the north and carving out a natural harbour at Kochi. The rulers of the Kingdom of Cochin moved their seat here, and the port drew traders from across the Indian Ocean.

The Portuguese arrived in 1500 and in 1503 built Fort Manuel, the first European fort in India, along with the church now called St. Francis — the oldest European church in India. Vasco da Gama died in Kochi in 1524 and was buried there before his remains were taken home to Portugal. Around 1555 the Portuguese built a palace at Mattancherry for the Raja of Cochin, later renovated by the Dutch and known ever since as the Dutch Palace.

In 1663 the Dutch captured Kochi, and the British took control at the end of the eighteenth century. Through it all, the town's Jewish community thrived: the Paradesi Synagogue, built in 1568, is the oldest active synagogue in the Commonwealth. The royal family of Cochin built the Hill Palace at Thrippunithura in 1865.

In the 1920s and 30s, harbour engineer Robert Bristow dredged a new island, Willingdon Island, to create a modern deep-water port. The district was formed in 1958. Since then Kochi has added a shipyard, the Kochi-Muziris Biennale (first held in 2012), a metro (2017), and in 2015 the world's first fully solar-powered airport.