A lot of people traveling to Japan have asked me about this question. With the high cost of Japan Rail cost, does the it actually save you money when travelling Japan?
In Japan the most convenient way to travel around is by train. Japan offers a huge variety of train passes that will allow you to save money. There are regional passes which make sense if you only stick to a certain region during your stay.
A JR pass must be used on consecutive days within its allotted time frame. That means a 7-day pass must be used in 7 days - after that, it will no longer be valid. A 7-day JR pass costs ¥29,110 (~$251 USD), or ~¥4,158 (~$36 USD) per day. Compare this against what you'd spend on transit per day in 7 days (and trust me there's lots of options!). It is potentially ideal for limited, fast-paced travel but works only on JR lines. For example if you just make one round trip between Tokyo and Kyoto on the shinkansen (bullet train) and use the pass to travel between Narita and Tokyo, you've already saved money with the pass. The cost of a normal one-way shinkansen (bullet train) ticket from Tokyo to Kyoto is Y13,080 and the round-trip fare is Y26,160. An ordinary one-week pass is Y29,110. A one-way trip on the JR N'EX (Narita Express from Narita International Airport into Tokyo) costs Y3020. Thus, if you use the pass to travel from Narita to Tokyo, then on to Kyoto and back, you've already saved money.
A JR pass can get you from one city to the next on a cheaper fare, but will not work on anything else. Local buses, subways, and non-JR trains must be paid for out of pocket and you should factor in those additional costs. If planned well then one can get cheaper flights or regional pass. For example, if you are visiting Tokyo and the Kansai area which includes Kyoto, Osaka, Nara, Kobe, Hyogo, Wakayama etc, a multi-day Kansai Thru Pass can be used in can be used on non-consecutive days and it also gets you discounted entry to multiple attractions. and between all of these cities. It also includes unlimited use of inter-city trains, subways, and buses and
Regional passes tend to allow more flexible planning. Passes can typically be purchased at Tourist Information Centres, which are common in airports and rail or bus stations as compared to JR Pass which has to be bought outside the country in advance. The various budget airlines in the region like Vanilla Air, Peach Air, and Jetstar offer very good prices if booked early, at times can be cheaper than trains or buses, so is worth considering for long distances. Willer offers buses passes from ¥10,000 for three days of travel within two months.
Create your potential travel itinerary and you can compare individual train prices in Japan with the cost of the JR Pass for your entire trip duration with the Japan Rail Pass Calculator.
If you'll be travelling at a fast pace to lots of places, especially on the expensive bullet trains, then it's likely that the JR pass will save you money. But if you are on a really tight budget and are travelling at a slow pace, taking the regional pass or buses could work out cheaper. So depending upon your itinerary and the kind of travel your prefer, the JR Pass can come handy or not. So choose wisely