The Jinnah International Airport is located in Karachi. It is the largest and busiest airport of the country. It handles 10 million passengers a year. The airport also receives the largest number of foreign airlines, a total of 35 airlines and cargo operators fly to Jinnah International predominantly from the Middle East and southeast Asia. All of Pakistan's airlines use Karachi as their primary hub including PIA - Pakistan International Airlines, Airblue, and Shaheen Air.

The city's old airport terminals are now used for Hajj flights, commercial offices, cargo facilities, and ceremonial visits from heads of state. US Coalition forces used the old terminals for their logistic supply operations as well. The city also has two other airstrips used primarily by the armed forces.

The largest shipping ports in Pakistan are the Port of Karachi and the nearby Port Qasim. These seaports have modern facilities and not only handle trade for Pakistan, but also serve as ports for Afghanistan and the land-locked Central Asian countries. Plans have been announced for new passenger facilities at the Port of Karachi.[34]

Karachi is linked by rail to the rest of the country by Pakistan Railways. The Karachi City Station and Karachi Cantonment Station are the city's two major railway stations. The railway system handles a large amount of freight to and from the Karachi port apart from providing passenger services to people travelling up country. Plans are underway to extend the intra-city railway system to play a part in the city's mass transit through Karachi Circular Railway system. Currently, primarily motorists and minibuses handle commuter traffic, but there are plans to construct a light-rail based mass transit system in the city to decongest the roads and provide quick service to commuters. Feasibility studies have been carried out and a provisional network has been agreed on. The unofficial working title for the proposed mass transit system is "Duz" (Urdu دوز), a contraction of the Urdu for "Underground Railway" (Urdu زمین دوز گاری).