Public transport in the city is largely dependent on private buses. Taxis and autorickshaws (called autos) are available for hire throughout the day. Narrow roads and the mix of vastly differing types of vehicles have made traffic congestion a major problem in the city. A metro rapid transit service, intended to considerably ease congestion, is planned for the city.

Because it is one of the safest harbours in the Indian Ocean, Kochi ranks among India's major seaports. The port, administered by a statutory autonomous body known as the Cochin Port Trust, offers facilities for bunkering, handling cargo and passenger ships and storage accommodation. It also operates passenger ships to Colombo and Lakshadweep. Boat services operated by Kerala Shipping and Inland Navigation Corporation, the State Water Transport Department, and of private ownership are available from various boat jetties in the city. The junkar ferry for the transshipment of vehicles and passengers between the islands are operated between Ernakulam and Vypin, and between Vypin and Fort Kochi. However, with the construction of the Goshree bridges (which links Kochi's islands), ferry transport has become less essential.

The Cochin International Airport, which is about 25 kilometres (15 mi) north of the city, handles both domestic and international flights. It is the largest airport of Kerala, and one of the busiest in India. It is the first international airport in India to be built without Central Government funds. A second airport run by the Navy also operates in the city.

There is no intra-city rail transport system in Kochi. The inter-city rail transport system in the city is administered by the Southern Railway division of the Indian Railways. There are two main railway stations—the Ernakulam Junction and the Ernakulam Town (locally known as the 'South' and 'North' railway stations respectively). The railway line connecting these two stations cuts the city longitudinally in two, with two narrow bridges connecting the two halves.