The city of Cochin may be said to have originated as an important port in 1341 AD when the flooded Periyar River destroyed a world-renowned port, Kodungallur, just north of Cochin and created an all-new harbor in Cochin, which is today one of the finest natural harbors on the West coast of India. Cochin's trade links with Chinese and the Arabs is reputed to be at least 2000 years old. Christianity in this city dates back to the apostle Thomas, who, as tradition holds and evidence supports, landed in India in AD 54 to spread the Gospel. There is also evidence pointing to the presence of Jews since at least AD 388.

Cochin's busy port assumed a new strategic importance and began to experience commercial prosperity after the flood. The Portuguese penetrated the Indian Ocean in the late 15th century. Vasco da Gama, discoverer of the sea route to India, established the first Portuguese factory (trading station) there in 1502, and the Portuguese viceroy Afonso de Albuquerque built the first European fort in India there in 1503. It was the first European fort in India. The British settled here in 1635 but were forced out by Dutch in 1663, under whom the town became an important trade center. It came under the sovereignty of Haidar Ali, the militant prince of Mysore in 1776, but was surrendered by his son Tipu Sahib to the British in 1791.

Legend holds that the Jews first settled in India during the time of King Solomon, when there was trade in teak, ivory, spices and peacocks between the Land of Israel and the Malabar Coast, where Cochin is located. Others put their arrival at the time of the Assyrian exile in 722 BC, the Babylonian exile in 586 BC or after the destruction of the Second Temple in 70 BC. No reliable evidence exists, but most contemporary scholars fix the date at some time during the early Middle Ages. The earliest documentation of permanent Jewish settlements is on two copper plates now stored in Cochin's main synagogue. Engraved in the ancient Tamil language, they detail the privileges granted a certain Joseph Rabban by Bhaskara Ravi Varma, the fourth-century Hindu ruler of Malabar.

At the beginning of the 20th century a modern port with dry docks and ship repair yards was constructed, and Willingdon Island (connecting Fort Cochin with Ernakulam and other townships by a Rail Bridge and road) was built from the dredging of the harbor's inner channels. After India's independence, Cochin became the major training centre for the Indian Navy. This city can also take pride of place when it comes to trading in spices, for which it has always been