Even though Japan is not a cheap country this guide will introduce you to how to travel Japan on a budget. We stayed three full months there, the whole duration of the free Visa, with around 1,500€ for two persons.
Our trip was done bicycle touring but most of this guide could be used by hitchhikers, walkers and all sort of backpackers with a little adventurous spirit.
Nothing could beat though the freedom of the bicycle, Japan it's a very easy destination for bicycle touring beginners so consider buying a bike.
Japan is way more than Tokyo, Osaka, Kyoto and slow travel it's the best way to completely experience this magic country. The real Japan is in the countryside and the small towns, and those are good places to go for a budget traveler.
This guide is based on our sole experience, so please contribute in the comments!
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We slept a lot in Jinja, or Shinto shrines. They are everywhere and you often can find a roof to stay dry and a water pipe, sometimes even electric plugs. Cemiteries are also another options.
Anyway we never really had problems in finding somewhere to pitch the tent (even though in the urban areas it could be hard and less nice, with highway bridges being a easy option).
Warmshower and Couchsurfing are widespread in Japan but many members don't speak English and so often are shy to host you. Give it a try anyway, we met very beautiful people.
Random host: to open his house to a stranger it's a very uncommon thing for a Japanese. Even thought we had been hosted by people we didn't know directly for almost a month in Tokyo area. The thing is, we may say, that a Japanese it's willing to offer his/her wonderful hospitality if you are introduced by somebody or first made friend with him/her.
Accomodation: hotels and B&B are crazily overpriced in Japan, this is where the stereotype of the expansive Japan becomes true. We hadn't checked that so much but saw nothing for less than 50€ for one room in a love motel. So much overpriced they are that outside the main touristic area you will see many abandoned hotels. Many Japanese prefer to sleep in the car for their weekend out. It's pretty common also for families.
There are secret free or super-cheap accomodations in the center of Osaka and Kyoto.
In Osaka there's a free camping spot in the Tsurumi Ryokuchi park (GPS coordinates: N 34° 43' 00.2 E 135° 34' 05.7).
In Kyoto you can stay at the student dorm for 200Y (1.5€), it's a dirty place but funny (Kyoto student dorm open to travelers GPS coordinates: N 35° 01' 41.5 E 135° 46' 42.2). So even in Japan, if you know where to look there's always chance to find super-cheap accommodations for those on a budget.
Restaurant though are not for the budget traveler, expect to pay 5€ for the cheapest bowl of ramen (Japene noodles in broth).
So, how do we experience the Japanese food on a budget?
No problems, there are many ways.
In the beginning it's easy to stick to combini (7Eleven, Family Mart, Lawson and other convenience stores).
They have a choice of bento (all kind of precooked food) that you can warm up in the microwave at the store, or have hot water if needed.
The food in this kind of places it's not so good but there's usually lot of choice of rice and meat, onigiri (rice balls), various noodles and even some "Italian style" spaghetti. Think at the convenience store as a all in one station: you have wi-fi, toilet, drinkable water, food and drinks, and not less important a place where to throw your garbage, almost impossible to find elsewhere. But you wouldn't experience much of the Japanese cuisine here.
Japan has among the best supermarkets in the world in my experience. Here you can find almost everything you are dreaming of. Most of them, not just the biggest, have a kitchen and they prepare their bento on the spot.
Stuff it's much more fresh here, it's very easy to find eight very good pieces of sushi for 3€. A lot of choice and more similar to what you could find in a cheap restaurant.
The secret hint? That one or two ours before closing time they will give from 20% to 50% discount on all the bento. Eight nice sushi for 1.50€? Not bad i would say.
And more than that you have all sort of ingredients from all over the world, and some are quite cheap!
Fruits and vegetable are infamously expansive but you always find up to 90% discount on expiring veggies and they are still good for one or two days. Not more they could live in my bags anyway.
We spent a lot of time in Japanese supermarkets figuring out how to get a great meal an we often succeeded.
Those are apparently big cosmetic and soaps shops but they always have a food department. Here you can find precooked udon and noodles for 17Y, sauces to dress them for 0.5€ (tomato sauce, carbonara, mushroom cream).
Sort of jam for your breakfast, frozen onigiri and other stuffs that will quickly de-froze in your bags. Also the cheap beer is to be found here.
Seasonal fruit and vegetables are easy to find for road travelers in the rural area, just beside the roads there are stalls with packs of them for cheap price, if there's nobody there leave the money in the box. This is Japan.
But the best and only real way to experience the real Japanese cuisine is to have a Japanese person cooking specially for you, so make friends! Japanese people can be very shy but they are warm in their heart.
Having a proper shower it's not hard, onsen and public baths are everywhere and can be very cheap, ranging from 1€ (even free in Beppu, maybe also elsewere). You can stay here as long as you want, until closing time (usually in the evening).
If you are in Kyushu during the warm season you can enjoy plenty of waterfalls and river where to rinse yourself from the sweat.
Free public wirless connection is not so common like in Korea.
Hitchhiking it's possible and safe but not super easy. Again the Japanese "shyness" maybe.