There are buses in the city, but are mainly used for traveling outside of the city, some of the bus companies that operate in Mombasa include; Mash Poa, Coastbus, Dreamliner, Spanish Coach, and Modern Coast Express. A one-way non-air-conditioned bus fare to Nairobi costs around Ksh 1000 and the trip takes 12 hours.

Matau’s are the major form of transportation in the city, 14 seater minibusses that ply the streets. There are around 3500 Matua’s in Mombasa, licensed ones have stickers on the windshields. They are the cheapest option for getting around the city with rides starting around Ksh 20 and upwards depending on the distance and time of day.

There is a modern railway station in Mombasa, the Mombasa-Nairobi Standard Gauge Railway which replaced the narrow-gauge Uganda Railway completed in 1901 under British colonial rule. The Mombasa Terminus station is located at Miritini and links Mombasa to Nairobi. The station is located about 12 miles from the city center. The Mombasa railway station is managed by The Rift Valley Railways (RVR) Corporation which runs overnight passenger trains to Nairobi twice a week. There are first, second, and third-class coaches, and they also run a cargo haulage service mostly used to transport cargo/containers from the port of Mombasa to the inland and vice-versa.

The 329-mile-long railway line from Nairobi was introduced in 2017 and reduced the journey time to five hours. There are state-of-the-art rapid trains that run, an economy class ticket costs about Ksh 1000, a first-class ticket costs about Ksh 3000. There is a new commuter rail system that links Mombasa Terminus with the old railway terminal in central Mombasa that is currently under construction and expected to open in 2024. The Mombas Terminus is 6 miles west of the city center, an impressive new station located in the western suburbs, with a connecting bus shuttle that runs to and from the old railway station in central Mombas.

Renting a car in Mombasa is a good idea if you want to travel outside of the city and explore the rest of the country. Driving in the city is pretty straightforward, the majority of the roads are tarmacked, and the Mombas-Nairobi Expressway connects Mombasa to the capital city of Nairobi and other parts of the country. It is not necessary to rent a car if strictly staying in the city as there are plenty of options for getting around.

There are official and unofficial taxis available in Mombasa, licensed taxis will have their papers stuck to the windshield. Always negotiate with the driver beforehand on a price for the ride, prices will depend upon the distance and time. There are shared taxis offered by Hakuna Mutatu Bus with journeys from Mombasa to the Kenyan Coast costing around Ksh 1000 for the 1.5-hour journey. The shared taxi is a door-to-door service which means you will be picked up from your accommodation/location and dropped directly to the next destination.

Uber, Taxify, Little, Mondo Ride, and MaraMoja is much cheaper options for a ride, simply download their app and get fares online.

Walking around the city is easily done on foot, walking around the city center, the beaches, and Mombasa Island will lead visitors to the main attractions. Connecting from the city center to the Island and other neighborhoods is not possible on foot, you will need to take some type of transportation to each destination, and then explore on foot.

Mombasa is the largest port in East Africa with 21 deep-water berths and two oil terminals. The port is connected by rail and road to the interior. There is little to no passenger service from the port, however, international cruise ships frequent the port.

There is a ferry route from Mombasa Island to the south coast operated by the Kenya Ferry Service from Kilindini and Mtongwe to Likoni on the south coast. The ferry has been deemed unsafe due to past accidents and incidents. There is a bridge being built to connect the Island to the coast.