You can find Japanese train routes and check timetables easily on a variety of websites and apps. Here are a few that we recommend:
Hyperdia: this website doesn’t provide any train times, however it’s still useful for checking travel routes and ticket fares. It also clearly displays results that show if a train route is covered by the JR Pass or not (JR trains are shown in green, while private (non-JR) trains are in pink), so it’s great for calculating if using a JR Pass will pay off for your trip.
Japan Transit Planner (Jorudan): This is one of the most reliable websites and applications for looking up routes, fares and travel times. The website displays JR Pass-friendly results under the “Rail Pass search” tab. Read our article about Jorudan here.
Japan Travel by Navitime: this website can filter route search results to prioritise travel by JR train, simply select “Japan Rail Pass” under the “Tourist pass” list before searching. It’s also available as a useful app (for both iOS and Android devices), enabling you to easily check routes while on the go.