If you are looking for the timetable of Shinknasen or major limited express trains, try to find it on JR Groups websites. Otherwise you can check the timetables on the following site, Hyperdia.
Hyperdia covers all railway lines and domestic flights schedule and fare table. This is the best website and help you to build your itinerary. It is simple but a bit tricky to use. Please wrote the guide of Hyperdia in the link below. Please refer it to learn more:
JR Group’s website
JR looks Japan’s National Railway but it was privatized long time ago. And technically there are five different companies, JR Hokkaido (Hokkaido area), JR East (Tohoku, Kanto, Tokyo and surrounding area, Nagano), JR Central (Shinkansen Tokyo-Osaka, Nagoya and surrounding area, Chubu region), JR West (Kansai and Chugoku regions), JR Shikoku (Shikoku area) and JR Kyushu (Kyushu area). These JR companies offers timetable and fare search in each websites.
JR Hokkaido offers very simple and easy timetable. You can pick the route and find all trains timetable. You can find all limited express trains and even local trains on major routes.
JR East timetable
This website show you the timetables of most of limited express trains, Shinkansen and popular seasonal trains in JR East areas. It also shows you the timetable of JR Hokkaido trains.
JR Central timetable
JR West timetable
This website offers you the fare and timetable of not only JR West trains but also many of JR trains.
JR Kyushu timetable
You can find the updated PDF format timetable. It shows you most of limited express trains, cruising trains and Kyushu Shinkansen.