Rural Japan is absolutely beautiful, I've travelled extensively there. The bullet trains are wonderful, but try going somewhere only the local trains go!

If you like biking, the Shimanami Kaido is unsurpassed.

https://www.japan-guide.com/e/e3478.html

Goes over multiple huge suspension bridges, grade-separated from the car traffic. In between the bridges you can explore the small towns on the islands in between.

To get there, go to Onomichi

https://www.japan-guide.com/e/e3475.html

which is a small city well worth visiting in and of itself. I recommend staying the night there, if you stay overnight in places that tourists usually day-trip to you get to see another side of the city. And when you're ready to hit the bike trail, you can rent bikes right there.

Further east, the Yamanobe Road is beautiful --

https://www.japan-guide.com/e/e4189.html

imagine walking all day through the set of My Neighbor Totoro, brought to life. Small towns, temples and shrines, mountain paths, small cities, and you'll walk by plenty of farms too. Easy to get to from Kyoto or Nara.

Further off the beaten path I recommend the Shikoku Henro Trail:

https://shikoku-tourism.com/en/shikoku-henro/shikoku-henro

If you have two months, walking the entire thing is the experience of a lifetime. But you can also spend just a few days (or one day) on the trail. I recommend starting at Temple #1 (they're numbered, this will be in Naruto, in the NE corner of Shikoku) and hiking for a day or a few days.

Japanese onsen -- hot springs -- are a great experience, look for a rotemburo, or open-air bath. Unfortunately most of these tend to be very off the beaten path, pretty well inaccessible by mass transit. But if you find one in your path, go!

You and your son are in for a treat. Enjoy!

I actually visited Japan for the first time this year, amazing trip. While I can't answer I highly recommend https://www.reddit.com/r/JapanTravel/ as a source of research. Great information.

I don’t usually see off the beaten path recs there, more like “how to see the best stuff as a first time / never again visitor”

As a Westerner, Japan was the first time I actually ever felt like a tourist/outsider. North America/Europe/Russia, you can sort of fit in if you're Caucasian and dont open your mouth; not so in Asian countries. It was an awesome experience.

Japan is great.

I recommend 3 things.

1. https://www.travelledmatt.com/miyajima-deer-island/. Not affiliated with the site but it gives a good synopsis of why you should go.

2. If youre going to the island, you might as well check out Peace Memorial Park in Hiroshima. A bit of a downer on a fun trip but totally worth it. Lots of tragically beautiful things.

3. Fukuoka. The first time I ever had traditional, authentic ramen it blew my mind. Now its an easy thing to acquire depending on your city/locale, but that is more semi recent. Still, I think about this one ramen shop I ate at frequently, like once or twice a month. That particular trip was a few decades ago now.

You don’t have to book with them but this Rakuten site can give you ideas of what’s available. https://experiences.travel.rakuten.com/destinations/japan/na...

Although Hiroshima is a big city, I would recommend visiting the Atom Bomb/Peace Memorial. You can visit the building that survived the bomb. A short ferry ride from Hiroshima is Miyajima Island which has Itsukushima Shrine. The shrine big Torii standing in the water is considered one of three most scenic spots in Japan. In Tokyo, if you don’t mind being crowded into a tiny room with giant sweaty men practicing sumo, I would pay to visit a sumo stable practice session and also pay for an interpreter.

My pointers are:

1. Learn the rail system and how to navigate it with the Japanese railway apps on a smartphone. I have seen too many tourists with looks of bewilderment at train stations trying to get somewhere.

2. Make every hotel reservation in advance. Most hotels here will not accommodate a person who shows up even if they have rooms available.

3. Most areas of Japan use different commuter passes so check ahead to see if you need a different pass for bus/trains.

4. Trains are nice but if you miss one you could be in a big wait or be later than you expected.

5. If you’re in the countryside you’ll be walking more or taking a taxi to get somewhere.

6. You may want to get used to ramen, soba and tempura as most of the near by restaurants will be offering this.

Aside from all this just enjoy the clean air and the view.

I’m very interested in this too! I went to Japan and a leg of my trip was to visit the Snow monkeys. I have never been as charmed by a place as I was Nagano. It’s probably because it reminds me so much of where I grew up in the California foothills, but I have an exceptionally vivid memory of walking along the Chikuma river and just being in awe of how peaceful it was.

For reference, I went during the peak of the cherry blosom season, and even though it’s a ‘tourist spot’, it seems like it’s out of the way enough that it wasn’t very busy, we only saw a handful of people. The train ride in was beautiful—no Shinkansen tho. The monkeys (which you take a bus to a hike to get too) were cute too! Highly recommended if you don’t find something better.

I’d only stop in Tokyo for the day, and continue up the country to Hakodate. The weather will change, there’s near no tourists and you’ll see a mountainous part of Japan that’s completely different to where else you’ve been.

Then on the last day that you fly out, go back in early - hit up whatever it is you’re going to Tokyo for (it’s not what it was in the 2000s, you have to search and get recommendations - the tourist trap area is just like any other large metro place in Japan) before flying out.

Get your luggage shipped to the airport.

Probably the easiest ski resort to get to is Gala Yuzawa. They literally have a train that goes right to the resort. https://gala.co.jp/winter/english/access-en/

Iseji, Nakasendo, Koyasan, etc. Stay at guest houses overnight along the way and eat well. Forward your luggage.

https://walkkumano.com/iseji/

Marriott also recently opened a bunch of hotels in rural / trail areas around Mie and Wakayama, as an alternative to guesthouses

How do you forward you luggage?

The Magical Japanese Art of Luggage Forwarding: https://craigmod.com/ridgeline/170/

(iirc this was on HN front-page a day or two ago, which might be why its top of mind)

same author as the iseji article above

Probably with Yamato. https://www.global-yamato.com/en/hands-free-travel/scene02.h...

I was in Japan last month. +1 for the Shimanami Kaido, had a great time cycling it. If you like tea, another highlight of my trip was this tour: https://obubutea.com/guided-tea-tour/

Shirakawa-go is amazing in winter and summer. The local homestay reservations had to be made very early. https://www.japan-guide.com/e/e5956.html

Also, any onsen city is worth going in the winter.

- Wazuka-Cho, near Uji City and Kyoto. Definitely off the beaten path. -Hakone -Shizuoka

All are related to tea farming and the great outdoors. If you haven’t been to Nara, I recommend there as well, there’s tons of wilderness to explore and it’s just a culturally vibrant place.

What kind of wilderness? And is it in the hills? Former hillman here :)

I vaguely remember reading about Nara, maybe in a National Geographic article.

But I don't remember what was said in it.

Consider starting a little further south with a trip to Yakushima.

Driving and hiking around the island made for a nice contrast to Tokyo.

The hydrofoil and a diy bbq at Sen's house made that part of our trip feel personal and remote.

I visited Japan in 2019 and Shikoku was the highlight. The Iya valley has beautiful nature. Kochi amazing food.

Read Alex Kerr's Lost Japan to get a good perspective on the Iya valley and Japan in general.

What kind of food?

While you want to stay away from tourist attractions, I'd highly recommend Todaiji Temple in Nara. It's an impressive structure and history but the deer will make it so memorable.

Is Japan a good place to visit for a more than short stay, for people who mainly eat plant-based food? Sorry, no offence meant to anyone.

I might be biased, but would recommend a pitstop in our sunny Miyazaki Prefecture.

See Miyazakian.com for details

YouTube is a great source for travel info.

Nikko is pretty cool.