Just a short post to be helpful to those planning a visit:
That Japan has one of the most efficient and advanced rail systems in the world is no secret. That Japan Rail offers ridiculously good value rail passes that can only be bought by foreign passport-holders outside of Japan is less well-known.
The scheme, setup to encourage tourism across the country, permits foreigners to purchase a pass for 7, 14 or 21 days. At US$540 for 21 days, these are far from cheap, however, they allow unlimited travel across the whole rail network and, in my case, saved me roughly US$1500 in travel expenses!!
The shinkansen (famous “bullet train”) is as rapid as the name suggests and you can go from city centre to city centre in a blink of an eye (as long as you blink very slowly). Clauses to the pass prohibit travelling on certain trains (Nozomi shinkansens, for example) but you will have more than enough options.
There are plenty of companies online through whom you can purchase a JR Pass but please remember to do it well in advance as it needs to be couriered to you before you reach Japan.
Other points to note: if you leave it in the seat pocket of a shinkansen (bullet train), you may end up travelling a long way out of your way to recuperate it. Perhaps I speak from experience…..?