When I travel as a visitor to Japan, I usually try to take advantage of the Japan Rail Pass and ANA Experience JAPAN Fare to save significantly on domestic travel within Japan (please see below). As a general rule, I use the rail pass if I am traveling frequently during a 1-3 week time frame and use the discount airfare if I am traveling infrequently or in a hurry. Keep in mind that all of these tickets are only open to foreign citizens or permanent residents visiting Japan and that in most cases these tickets need to be purchased in advance prior to travel to Japan and are non-refundable.