Japan Railway Pass (https://www.jrailpass.com/)
No Japan trip is complete without a JR Pass. Using trains is as easy as using a subway in any city of the world. From journey times ranging from half hour to up to five hours, bullet trains connect all corners of the country. The pass is specifically designed for tourist and can only be bought outside of the country before arrival. A valid visa is required for purchase, which will also be checked at the time you exchange your voucher for the pass at the Japan Railway counter.
JR pass will start saving you money from the first trip itself. Stations are located centrally and are easy to approach. Frequency is enough for you to make a pretty flexible plan just in case of any last-minute changes. It includes all Japan Rail National Train, Shinkansen (Bullet Train), Airport transfers, as well as JR Buses and Ferry. Which basically means one pass to solve all your travel issues.
Even if you just do a Tokyo- Kyoto round trip the JR pass it will save you money. Though round ticket from Tokyo to Kyoto will cost 26200 Yen approx, but combined with subway and other modes of transport and convenience, it is value for money
Where to Buy?
JR pass is sold under two categories namely Standard and Green Pass -First Class.
The main advantages of a Green pass are:
More Leg Room
Luxurious and comfortable seats
Fewer Crowds (hey it's more expensive)
In peak season it'll be easier to get a seat with a Green pass as fewer people buy it
They have options for 7, 14 and 21 days. Special discounts for kids and senior citizens. JR pass is delivered free of cost to the comfort of your home within 24 to 48 hours. If it is a last-minute trip you can buy it from an authorized travel agent in your city too. Insist on the free Japan travel guide with it.
Click on the links below to Buy now
https://www.jrailpass.com/
Viator
Travel agents in your city. Most of the times would deliver at your home for free of charge.
***Note: Has to be bought outside Japan before arrival.
How to use your Japan Rail Pass?
Once you have booked your JR Pass a printed voucher will be delivered to your address, carry that when you fly into Japan.
Steps to get started:
As you land on Narita airport ask for directions to JR East Travel Centre.
Exchange your voucher for a JR Pass - A valid passport and visa to be shown with the voucher.
JR pass can be activated immediately or within 3 Months of exchanging the voucher.
There is an Option to get your seat reserved to avoid any last minute confusion. Especially on national holidays most trains are fully reserved in advance
You are all set to use the Airport transfer to Tokyo, Subway, Ferry and of the amazing Shinkansen (Bullet Train).
While entering and exiting the station look for a Manned Gate. Show your pass to the officer in charge to pass thru (as you don't have a ticket for machine or a card to tap on the sensors).
Locker facility
If you are planning to travel multiple cities and have packed itinerary, lockers are the answer to your problem. They have thought of everything and made it easy, like the Coin Locker facility at train stations in Japan.
Depending on the size of your luggage choose an appropriate locker and make payments by Suica or Cash. The machine accepts payment for a day and will recalculate the amount at the time when you take your luggage out on the basis of number days the locker was used.
Train Stations
Japan stations are a destination in themselves. They are massive with multiple levels dedicated to restaurants, takeouts, bakeries and great shopping options.
Tip: Reach the station an hour earlier to grab a meal before your trip or get an Ekiben (Bento Box) of your choice to have it later on the train.
Japan - Access and Transportation
http://www.japan-guide.com/e/e2363.html
A complete guide to access and transportation in Japan