The city is served by four tram lines or streetcars that service the entire city from 6 am until 11:30 pm with trams departing every 10 minutes. The lines are color coded and the cost of a single ride is around ¥120 with 1-day passes available for ¥500 offering unlimited travel within one calendar day, the passes can be purchased at the JR Nagasaki station and at major hotels in the city. Line #3 Red and Line #1 Blue run along the same track from the north and the blue line continues to the You-me Plaza shopping mall.

The city is a great place to navigate on foot with the city center and many of the tourist attractions situated on flat terrain. The city center runs north to south on almost a straight line that borders the Urakami River and then borders the east side of the harbor. The size of the city makes it navigate-able on foot with an easy layout providing a good layout for exploring the heart of the city and other popular attractions. The tram stops are located all around the city and it is a short walk from any tram stop to get to most anywhere else in the city.

Nagasaki is serviced by a number of city buses that run all over the city and cover a wider area than the trams do, however they are not user-friendly for non-Japanese speakers.

You can rent bicycles at the JR Nagasaki Station from Eki Rent-a-Car which are electric powered bicycles which makes it easier to explore the hills in the city. The city of Nagasaki features many rolling hills and can be hard to navigate on a bike unless you are used to a vigorous uphill terrain. The city center is mostly flat terrain and is easiest enough to navigate on a bicycle.