Transportation Across Japan
Trains and Subways
Since most tourists use train and subway to travel around Japan there are many websites that will give you the best route from one station to the next. My favorite is Hyperdia which offers timetable and route search for railways in Japan, in Japanese, English and Chinese. There is also Japan transit planner Jorudan. Between these two I think it is a matter of preference as to which you prefer using.
City Buses
The buses run very infrequently out in the country. I have not found a website that has bus schedules in English. Since bus information can change I suggest you use www.navitime.co.jp. Sometimes google maps will tell you if there is a bus stop, and the correct times. I found that while google maps works well in larger cities in the countryside it becomes more unreliable. I have also had some success with google maps while hiking, depending on the popularity of the stop it would pop up on the maps, as would the times. This method was not consistent, which is why I recommend www.navitime.co.jp. The down side is that this website is completely in Japanese.
https://www.navitime.co.jp/bus/
Riding the Bus:
Riding a bus seems pretty self explanatory but the bus in Japan may be a little different than what you are used to in your home country. Most guides are centered around navigating Tokyo, and about how to use the Japan rail passes on buses. Small town Japan and the transit you’ll experience are worlds apart, some areas that you go to don’t even have bus stops. There are only names of locations which you give to the taxi company listed on the sign so they know where to pick you up! The Tanabe city has a great explanation on how to ride a local bus, along with pictures, I have linked to that website. I suggest familiarizing yourself with the how to before you go.
Highway Buses
Highway buses are a great way to travel long distance in Japan. The highway bus Japan site helps you make reservations in English.
I have taken the highway buses many times during my trips to Japan, and have used both services listed bellow.
Highway Bus Reservations- https://highway-buses.jp/
Willer- http://willerexpress.com/en/
This information is taken from tokainaturetrail.com and Hiking the Tokai Nature Trail: A complete guide.