8/31/15: This page is still under construction. Please check back for future updates!
Traveling by train in Miyazaki is a little more expensive than elsewhere, but also very handy and reliable. You can use the normal trains (slower because it stops at every station on the way to your destination), the limited express and express trains (only stop at key and major stations, and much faster but also more expensive). For a neat if pricy thrill, the Kyushu Shinkansen (新幹線, ‘bullet train’) runs between Kagoshima and Fukuoka (and even all the way to Hiroshima or Osaka!) More about Kyushu’s rail network here http://www.jrkyushu.co.jp/english/
A useful site for checking train schedules and fares is http://www.hyperdia.com/en/
An alternative site: http://www.jorudan.co.jp/english/norikae/
Printed train schedules are also available for free at bigger train stations.
PLEASE NOTE: During the major vacation times (3 times a year), residents of Japan can buy a Seishun18 Ticket. This allows the holder to have five one-day unlimited travel passes to use for select trains across Japan. Bullet trains are excluded. The 5 passes are valid during the vacation period, so they don’t have to be used on consecutive days. The cost is only 円11,500. Also, the 5 passes could be split between a pair or group of travelers. To find out more, click http://www.essential-japan-guide.com/seishun-juhachi-kippu/ or http://www.japan-guide.com/e/e2362.html.