While once only limited to big cities such as Tokyo and Kyoto, you can find stylish hostels offering hotel quality accommodation even in rural Japan.
Many hotels offer single room accommodation for solo travelers at a reduced cost.
With dramatic increase in the price of Japan Rail pass, explore various regional rail passes offering unlimited train travel in a selective regions.
Benefit from airfares only available to international visitors offering fares as low as USD 70 for one way to any destination in Japan - ex: Discover Japan Fare of ANA.
You can visit my Japan based travel blog.