Check out Two Wandering Soles for great advice on preparing for your first visit to Japan.
Tokyo by JR Rail
The Japan Rail Pass covers the JR train lines in the city of Tokyo itself. The Yamanote Line does a convenient loop around the city with stops in all the major neighborhoods. You can simply hop on and hop off with your JR Pass by flashing it to the station attendant on your way in. We 'spent' one day of our train pass exploring Tokyo.
Tokyo to Kyoto by Train
For long distance rail trips on the Shinkansen, it's important to reserve seats before boarding the train. We had planned our itinerary in advance and knew what trains we needed so we stopped at the JR office in Shibuya station in Tokyo to pick up our seat tickets (free but must be reserved in advance). Tickets in hand, we boarded the high speed train to Kyoto. Kyoto is a gorgeous spot that gives you the opportunity to get away from the manic urban centers of Japan to experience a bit of Zen in the region's countless temples. As an added bonus, visit during Autumn foliage season like we did and experience some of the most vibrant colors you'll see in your life.
For more on the Autumn foliage, check out my post on the top temples to see beautiful Fall colors in Kyoto.
Riding the Rails from Kyoto to Osaka
We traveled from Kyoto to Osaka with our JR Pass. We really enjoyed Osaka as it is a foodie and shopping mecca. It's also cheaper to stay in Osaka than Kyoto and is an excellent home base for day trip exploration.
A Day Trip to Hiroshima by Rail from Osaka
While we based ourselves in Osaka, we took the opportunity to use our 7-day Japan Rail Pass for a day trip to Hiroshima. There is a heart-wrenching museum detailing the effects of the war and atomic bomb dropped on the area. The peace park is also quite moving with thousands of folded paper cranes showcasing people's hope for lasting peace. The skeleton of the building at 'ground zero' remains a ghostly reminder of what happened here in the name of ending World War II.
Travel from Hiroshima to Miyajima Island by Train
Miyajima Island is not far from Hiroshima and we used our JR Rail Pass for the train and ferry required to get there. The island (aside from the throngs of tourists) is quite serene and it's possible to find a quiet spot to reflect on the iconic Torii gate as the waves lap gently onto the shore.
Osaka to Nara by Train for a Day
Nara is another easy day trip from Osaka with your 7-day Japan Rail Pass. The Nara area is known for gorgeous wooded temples and armies of deer. It's possible to buy 'deer cookies' to feed these fellows but beware, they can be quite aggressive as you can see from the warning signs posted around Nara highlighted below.
We saw a lot of the country in a limited amount of time. If you have the luxury of more time, here are some ideas for a 2-week itinerary in Japan.