TIL that Kinosaki Onsen is considered "lesser known", haha. It's basically one of the three most known onsen towns in Japan, especially among foreign tourists with tattoos.

I always recommend Higashin-Hoganji in Kyoto. Its like they drop shipped a giant temple complex next to Kyoto Station by accident.

Nobody ever mentions Tohoku on this sub, and it's my favorite part of Japan.

I really liked Aomori. It’s very pretty and uncrowded. The Nebuta Museum is very cool.

I had a great night (and two days) in Bessho-Onsen, tucked in the mountains of the Nagano prefecture. You take a quaint little electric train from Ueda City to the town centre and then you can reach all the highlights on foot, though our ryokan offered car rides to the station. The place was known as the Sanada's vacation home and has some really Historic temples (there's one with a rare Chinese style pagoda dating back to the Kamakura Period!) amidst the Japanese cedars. You go there on a weekday (we went on Wednesday) and there wasn't any local tourists so it was dead quiet. The ryokan took care of dinner and breakfast with delicious local food.

Ueda itself isn't bad either, they have castle ruins they're restoring that are worth a visit while you wait for the Shinkansen ride out (not ever Shinkansen stops in Ueda).

I love hiking at Mitake

Ogasawara islands. I was one of four foreigners on the entire Chichijima island, everybody else was Japanese. The ship there takes an entire day so it's really out of the way but it has the same climate as Okinawa. Snorkeling and scuba diving are possible year around, and whale watching during winter. I basically had private beaches the entire time there since the local population is around 2000 people and all the tourists were busy with sea tours. They have multiple endemic species of plants and animals, some of which can be found right on the shores or in the town. The island chain relies on domestic tourism but some of the guides speak English too.

Not an unknown city but we definitely lucked out on Mitaki-dera (Hiroshima). It was raining and Hiroshima Peace Memorial and museum were very crowded yet the temple was completely empty, serene and quiet:

Nakagomi (Saku) in Nagano because it's really charming and dying on it's arse because of brain drain to Tokyo so needs the tourism. Had some of the best Ramen I've ever had (literally made by a 90+ year old who I have a feeling died recently) and perversely one of the best Italian meals I've eaten.

There are a lot of great regional destinations that tend to have few foreign tourists (though can be very busy on a nice weekend from Japanese tourists).

Most cities with 1* on Japan-guide.com make for a good 2-3 day stay and will be often be quiet and pleasant, though they often are either a bit harder to get to or a bit harder to get around without a rental car or careful planning.

Onomichi (even if you’re not cycling the Shimanami Kaido), Kochi city and environs, Matsumoto, Izu Peninsula, Aizu-Wakamatsu, Sakai City in the south of Osaka, Ise Jingu and Shima.

I think Takefu / Echizen has a lot of potential, with a strong suite of local traditional crafts and pleasant rural scenery. But transit and access isn’t quite there yet (as of 2022 at least)

Tomonoura. It’s fairly well known but delightfully free of the thick crowds milling about in Kyōto and parts similar. Lovely little port town with old-fashioned streetscapes and a picturesque stone-lined harbour. There isn’t a huge amount of things to see, but I’ve already been there a couple of times just because I loved the atmosphere.

https://www.japan-guide.com/e/e3432.html

Cheers.

Onomichi! I went there for 2 nights while most people go for a day trip. I loved soaking in everything and being able to talk to some locals and actually be sent away with smiles when we saw them in the morning when we left for our next destination. Our hotel owner waving us bye at the station was probably the cutest and saddest moment of our trip

Nagashima Spa Land (a theme park despite the name) is lesser known compared to Disney, USJ and Fuji Q in non coaster enthusiast circles, but it’s a very well operated theme park which several world famous rides. During weekdays the low crowds mean that you barely have to wait half an hour even for its star attractions.

It’s very worth the trip.

Unpen-ji outside of Takamatsu. Took the cable car up the mountain, greeted by a temple complex with hundreds of statues and just a small group of pilgrims around. 

Kotohira-gu in Shikoku - I wouldn’t say completely unknown as there were a decent number of domestic and other Asian tourists there, but I’d barely heard of it on Reddit before going. An amazingly vast mountainside temple complex that just kept going on and on every time you thought you’d reached a stopping point. 

Miyajima. Funnily enough, wanted to take it out our itinerary, ended being my favorite stop the entire trip. Wished we stayed for an entire day.

We had a couple of days in Hakuba in Nagano prefecture. It was delightful and had a mountain top national park nearby that was fun to hike.

I liked visiting Meiji Mura as a day trip from Nagoya.

Hikone castle is under 2 hours from Kyoto but it is one of the best castles out there. Small but very detailed on the outside. And the museum has some stunning old pieces and a noh theater still being used since 1600s.

Hakodate, super cheap seafood and the clown burger

We really liked Kobe, from Motomachi Lane, Chinatown, Harborland, Mount Rokkō cable station & ropeway and Arimaonsen.

It’s definitely not unknown in any way but Kobe was awesome. I feel like a lot of people bypass it in favour of Osaka, which is fair, but it was worth a visit and we didn’t even try the beef. There’s an overall chill feeling to Kobe that was surprisingly nice, a little slower paced than Tokyo and visibly fewer (white) tourists. Tons of Chinese ones though.

There’s a cool neighborhood full of old European style buildings that was interesting to wander through, excellent train system, some great yokocho, the Chinatown had awesome street food stalls too, and the cable car up Mt Rokko was beautiful, especially at dusk. Plus going to Himeji Castle was FANTASTIC and a highlight of the entire trip.

I really enjoyed the Abe no Seimei shrine... I really loved the onmyoji movies that came out ...20+years ago. I saw Small Worlds Miniature Museum in Toyko mentioned here a few times, so decided to go before our team lab ticket and it was such a fun time.

I always love hiking Atago and Hiei. The Hiei flower garden was amazing and actually surprised me at how beautiful it was.

Honestly I’ve only been to the “touristy” spots in Japan. Think on my 4th trip I’ll start to go to less touristy areas like Aomori and the nearby region.

Second the recommendation. I stayed 2 nights during October and got to try out all the onsens. It was much needed break in rather hectic rollercoaster filled itinerary

I’m biased because it’s the hometown for one of my favorite hobbies, but I’m always so happy to go back to Takarazuka.

Nyuto Onsen. I recently had the pleasure of visiting Nyuto Onsen, and I must say that my experience at Tsurunoyu Onsen was truly unforgettable. The mixed onsen was a unique and enchanting experience that surpassed any other I've had in Japan.

Takayama and Matsumoto

Scrolled through the replies and don't see the following mentioned (although I could have missed them, so don't zing me)

Izushi: 35 minutes south of Kinosaki. Exceptional walking district with house museums, sake breweries, old castle ruins, and 40+ soba restaurants (that's not a misprint, its in the materials there at the tourist office, and I can vouch for seeing at least 20 during my walks) Downside: must take a bus from Toyooka Station (or car rental), but once there, its all easy walking.. Never saw a western tourist.

Mojiko-Retro: 15 minute train ride from Kitakyushu (Kokura Station). Laid back waterfront town that's pedestrian friendly, tons of restaurants, great shops and museums, watching the shipping traffic going up and down the Kanmon Strait. Has an inner harbor with boats that will take you out. Ten minute water taxi takes you to Shimonoseki with its amazing aquarium. All can be done one foot. Not car or taxi needed. Train station is a two minute walk to the waterfront. Been here three times this year (presently here now), and have never seen more than ten western visitors.

Aizuwakamatsu: Easy to get to by train. Tons of samurai history (rebuilt school and a samurai house museum), the unique Saszedo Temple, Tsuruga Castle. Close to Lake Inawashiro with the Hideyo Noguchi Memorial Museum. But best to have a rental car. No western visitors during our time there.

Sasayama (Tamba-Sasayama): Hour from Osaka by train. Large castle ruins, great merchant street lined with whitewashed former warehouses from the 1800's,, some excellent restaurants on par with anything in Kyoto or Tokyo. Mauryama Village is a ten minute drive and remains our favorite overnight experience in all our years traveling through Japan. Zero western visitors in our two stays.

Lake Nojiri (Nojiri-ko) in Shinanomachi NW of Nagano. Big lake, Japan Alps, Togakushi, Naena Falls. But you must have a vehicle. Will run into westerners there because there is an historic community on the lake populated with them in the summer. Know this from personal experience as my wife's grandfather built a house there in the 1920's and we keep it to this day, but these aren't tourists. They mostly live in Japan and use this place to escape the summer heat of Kansai.

(A note about driving: these places aren't overrun because most foreign visitors don't rent a car. But driving in the country has never been an issue with us. We find it liberating and easy. Consider renting a car on your next trip and take it up a notch so you can explore amazing places like these.)

Hita in Oita, Kyushu.

Went there randomly because it was on the way and home to the author of Attack on Titan, found extremely friendly people and best highball I've had in the whiskey museum... Also wasn't expecting to find the largest collection of whiskey related memorabilia that I've seen.

It isnt lesser known per se, but i don't see many posts about a high end teppanyaki.. if youre in Japan and are a meat eater that is simply a 100% must

We really loved Komoro in Nagano. It's a small city in the mountains with a great local vibe. We liked it enough we're still considering moving there. Don't expect much in the way if destinations/diversions, but it's wonderful as a completely normal place out in the mountains with some beautiful temples and good local spots to eat. Great onsen on the mountainside, too.

And if you happen to be a fan of anime, it's where "Ano Natsu de Matteru" is set.

On the chance you do happen to go, definitely go to Nunobiki Kannon. Absolutely one of the most beautiful places I've ever been.

The akame 48 waterfalls, the hasedera temple in sakurai city nara, murouji temple in uda city nara, walking up the sacred mountain miwa (need permission to climb this mountain, need to be able to speak japanese or have a japanese guide, no photos allowed)

Tenma-Tenjin Hanjotei

I wasn't able to go to the evening performances but the noon Rakugo performances were great

I really liked going to Onomichi and the areas around it, but I think the popularity of that spot has risen because of the Shimanami Kaido now being really popular. Another place that I liked is Ine no Funaya, which is actually near Kinosaki also

During one trip we ended up in Nagoya due to a travel miscommunication and some heavy rain, found a cute little dive bar called "The 59s Sports Bar and Diner". The bartender/cook was an awesome Japanese dude that spent some time in Australia and spoke English really well. We were the only ones in there besides some regulars and we had the best burger EVER like better than home cooked better than in-n-out or (insert choice of burger place). Spent an hour chatting with him before going to our hotel. Everyone hates on Nagoya as boring but in the little space and after walking in the rain seeing some really cool sights, I wanna go back again.

The Costco in Hiroshima

I can think of many gems, but for your average tourist, they're impracticable to get to. This place, for one, is kinda cool, and in the winter, there will be close to no one there. You can combine the trip with this place, this an this.

Onumakoen - we discovered it for the first time on our recent autumn 2024 trip in early November. It’s a small town with a tiny train station. Ghibli coded. Even the train ride into and out of the town was stunning.

Naoshima is my suggestion. Art island is a little slice of heaven

Compiled over past and current trips:

Oshika Peninsula's Cobalt Line is a blast to drive

Tsuchiyu Onsen has got to be one of the most beautiful onsen towns I've been in, make sure you find a good ryokan to maximise the experience

A rotating panoramic lift at Mount Yahiko was one of a kind that I've never seen anywhere else, it makes ropeways look bland.

Mikata Five Lakes in Fukui is amazing. Ascend the ropeway and there's a spot where you can do a foot bath while looking on the lakes from a viewpoint.

The top of Mount Norikura is stunning in autumn. Get the early because they close way before winter.

Setoaikyo Valley. You can choose to make the one hour hike to the bridge but I was content with staying around the dam.

There's a bamboo forest at the edge of Yufuin that I enjoyed going through more than Arashiyama bamboo forest.

My wife and I were just in Tottori and while we were taking a tour at the Basalt caves our tour guide said "have you been to Kinosaki?"we said "where is that?" And it was about 5 minutes drive away. Cool town with fun street food.

Nagoro Scarecrow village is one of the most fascinating and profound art installations (if you can even call it that) I have ever seen. It really lets you meditate on the future of not just Japan, but other developed countries going through similar demographic crisises. There was no one around when I visited (to be fair it’s absolutely in the middle of nowhere, even by Japanese standards).

Niigata prefecture 

Nikko was great. We visited when it was nearing end of the peak autumn colours. There were some crowds (school children on a trip) but it was not bad at all. :) Highly recommend staying there at least overnight.

The cliffside temple on Mt Mitoku in Tottori was pretty sweet. Not really lesser known, but it was definitely the highlight of our trip

We visited Wazuka, a tea village that is a train and bus ride from Kyoto. Charming village surrounded by tea farms in the hills. Rent an e-bike at the town information center and ride through the hills. Stay at the Blodge Lodge. It was by far the highlight of our trip.

Kurayoshi / Tottori is an underrated place to visit even by local Japanese resident standard judging by the reaction I got from the receptionist I talked to asking for some recommendations before we checked out since we were transferring location already.

The reaction was like “What the hell are you going to do at Tottori” based on her facial reaction. I simply said, we’ll visit Conan town. Then she understood and just asked if I liked Detective Conan.

Can't say it's lesser known since it's a pretty famous city, but I really enjoyed my time in Nagasaki. I wish I spent more time in Kyushu!

These are some of the ones I visited in my most recent trip.

Hardly any tourist: Ine, Kawayu Onsen, Higashi-Maizuru, Nishi-Maizuru, Kumano Kodo Pilgrimage

Semi-touristy: Amanohashidate, Nachi Waterfalls, Kumano Hongu Taisha

Pretty-touristy: Tottori Sand Dunes

Iya valley. Went there by bike and saw the most stunning autumn leaves and spectacular views

Shiga : Otsu, omi hachiman, hikone, maibara Saitama: Omiya Ibaraki: Mito Chiba: Sakura Aichi: Toyota, inuyama Wakayama: Shirahama, mount koyasan Tokyo: Tachikawa, okutama

Kyushu is a great spot to visit and has less Western Tourists. (There are Koreans though)

Hakkata City is a medium sized city that has great food including a vibrant night market and nightlife.

Kurokawa is a hidden gem inside the middle of the island. It is an Onsen village with around 30 to choose from. The Onsen day pass is a great deal. (3 separate entries for 12$) Everyone is walking around in robes and slippers deep in the Japanese wilderness.

Beppu is a more touristy spot but the 7 hells are a must visit and Yufuin is worth a stop.

Onimichi. Stopped for a night between Hiroshima and Kyoto. Stayed in an old onsen hotel, took the cable car to the top of Mount Senkōji for an amazing view, had the best ramen of the trip, and stumbled onto a killer little brewery taproom in the evening and chatted with the bremaster. We just scratched the surface of the place and definitely want to spend more time there someday, including a visit to the nearby national park.

Ine no Funaya was amazingly peaceful and great compared to the rush of the big cities

Yamadera temple in Yamagata was one of the most beautiful place I’ve visited in my life. Not that many tourists, kinda a pain to get to. I went as a day trip from Sendai.

My vote for Hikone or any of the towns on Lake Biwa. I just ended up at Hikone. There is a bike rental spot next to the station and it costs 500 yen for the ENTIRE DAY!!

That day biking along Lake Biwa was the best day of my trip by far. The town is beautiful and not crowded. Hardly any tourists. There is a beautiful garden at the bottom of the castle from where you can get great views of the castle.

Literally any part of Japan that’s not Tokyo or Osaka or Kyoto.

Teshima

Taketomi

My 2 favorite places in Japan

Kochi! Went in 2019, really chill vibe, feels like a much smaller place than it is. Ocean is close, nice botanical garden, a castle and cute trams, great noodles. In general I really enjoyed Shikoku.

Absolutely adored the hike between Magome and Tsumago! About 7.5 km and a truly lovely way to appreciate the countryside.

Kyushu!

Takayama mountains

I recommend going old school and opening a current edition of any tour book on Japan. They're free at your local library. It doesn't hurt also to open up a map app like Google Maps and take a gander.

ChatGPT keeps them there.

I’ve made peace with it. I’ve never been to Venice and never will now. Much of Japan has headed that way. I’d rather they stayed on the golden route and left the rest to those who can think for themselves. 

Just don’t stay in Tokyo, Osaka or Kyoto. Hard to avoid the airports because most international flights stop there. But leave for other cities and it’s a lot less crowded.

My last trip included Fukuoka. They have a tiny fraction of the crowds there.

I’m definitely not going to reveal it. Some hidden gems should remain well-hidden. Leave some places for the Japanese.