By plane
Kumamoto has an airport, recently renamed the Aso-Kumamoto Airport, from which shuttle buses make a one-hour jaunt into the town (�670). There are flights to and from Tokyo Haneda, Tokyo Narita, Osaka Itami, Kansai International, Chubu International, Matsuyama, Naha, Amakusa, Shizuoka, and Seoul.
If arriving at Fukuoka Airport, there is a highway express bus service (named Hinokuni-go) that will bring you to Kumamoto for �2000 and takes roughly 2 hours. Alternatively you can take the subway to Hakata Station and take the JR Kagoshima Line (see below).
By train
Kumamoto is a major stop on the Kyushu Shinkansen. Trains run several times per hour from Hakata station in Fukuoka (40-50 minutes, �4990) and Kagoshima (50-60 minutes, �6760). Hourly Sakura services connect Kumamoto to stations on the San'yo Shinkansen: Hiroshima is about 1 hr 45 min away (�12970), Okayama 2 hr 30 min (�16230) and Osaka 3 hr 20 min (�18020). Faster Mizuho services also run during the morning and evening hours, but Japan Rail Pass holders cannot use Mizuho trains.
From Tokyo, Kumamoto can be reached by train (a combination of Nozomi and either Sakura or Tsubame) in as little as 6 hours. Japan Rail Pass users can travel from Tokyo to Kumamoto in 7 hours using a combination of Hikari and Sakura trains.
Local trains from Fukuoka take 2 1/2 hours to reach Kumamoto (change in Omuta) at a cost of �2,070.
In addition to the central station, JR operates a second at Kamikumamoto just to the north, near the Fujisakidai baseball ground. Streetcars into the city centre also connect from here.
By ferry
If you're coming from Nagasaki, the numerous ferry services may be preferable. One such route invloves travelling via Shimabara. Take the JR line from Nagasaki city through to Isahaya then switch to the private Shimabara line. Its not JR but don't go through the ticket gate to get there, its tucked away on Platform