Hidden Gems and Secret Spots in Japan You Can’t Miss

Last Updated on 18th July 2024 by Sophie Nadeau

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Japan is a fantastic country where old meets new and ancient traditions meet cutting edge technology. It’s a country roughly the same size as California with plenty of historic temples, buzzing modern cities, and everything in between. And if you’re looking to get off the beaten path? Here are the best hidden gems and secret spots in Japan.

Hidden gems of Japan

Kinosaki Onsen

By Erin of Neverending Voyage

Onsen towns are a uniquely Japanese experience and perfect for a relaxing break soaking in the steaming waters of hot spring baths.

Kinosaki Onsen is ideal for your first onsen town. It’s under the radar for most visitors to Japan, but it’s foreigner-friendly (with signs in English, and unusually, tattoos are allowed) and only 2.5 hours by train from Kyoto or Osaka. 

Staying in a ryokan (traditional inn) is a key part of the experience (Morizuya Ryokan is a great option). You’ll sleep on a futon and enjoy delicious multi-course meals served in your tatami mat room. 

The ryokan provides a yukata (cotton kimono) and geta (wooden sandals), which you wear to stroll along Kinosaki Onsen’s picturesque canals and hop from one onsen to another. 

Kinosaki Onsen has seven public onsens, all included in the free pass you get with your accommodation. They all have a different character—some are small and intimate, while others have multiple baths (and even saunas) to enjoy. Many have pretty garden views.

Mandara-Yu is the oldest bath in Kinosaki Onsen, dating back to 720 AD. Goshono-Yu, in a temple-like building, is one of the most attractive onsens, especially the lovely stone outdoor bath with a waterfall.

It’s essential to familiarise yourself with onsen etiquette before your visit. You must be completely naked and shower thoroughly before getting into the bath. Public onsens are divided by gender. 

Some hotels also have private onsens available for mixed-gender use, which are a good place to start. 

Once you get over any initial apprehension, it’s a wonderfully relaxing experience. 

Spring (usually early April) is an especially beautiful time to visit Kinosaki as the cherry blossoms are in bloom along the canals. It’s much less busy than Kyoto, so you can enjoy the blossoms without the crowds. 

Naoshima Island

By Jonny of Backpacking Man

Naoshima Island, also known as Naoshima Art Island, is one of the most surreal places to visit in Japan. Located in the Seto Inland Sea, it’s known as one of the main modern art spaces of Japan, with many strange art sculptures to see outside, as well as some contemporary art museums.

Mush of these art spaces came from the Benesse Corporation and the must-visit museums when there are the Chichu Art Museum and the Lee Ufan Museum. If you visit during Spring, Summer, or Autumn, the Setouchi Triennale contemporary art festival may be on.

It’s just not the art that makes Naoshima one of the best places to visit in Japan. It’s rural vibe, with laid-back beaches and a timeless feel is another side to the island that many visitors miss out on if only coming to see the art.

One of the best ways to see Naoshima, especially to see the randomly scattered art pieces dotted outside around the island, is to rent a bicycle.

You can rent a bicycle from rental places at the main port of arrival. Apart from Naoshima, there are several nearby islands worth exploring, although you will need more time than just a day for a visit to these.

You can stay in Naoshima at hotels and guesthouses, but it’s also easy to do as a very long day trip from the cities of Okayama, Hiroshima, Osaka, or even Kyoto, due to the rail links to reach the ferry port for the island. If you do this you will be rushed though to see everything.

Shirakawago

By Chloe of Chloe’s Travelogue 

Shirakawago is one of the best-hidden gems in Japan that international visitors have only recently travelled to. This tiny town with less than 600 households is nestled deep inside the mountainous Hokuriku region and tucked away from any spotlight…until it became a UNESCO World Heritage Site in 1995.

The quiet farm village’s most culturally valuable property is the 300-year-old gassho-zukuri, traditional Japanese farmhouses with a thatched roof. With the Japanese Alps as a backdrop, they create a picturesque scenery similar to beautiful towns in the Swiss alps.

Mountain farmers still live in these heritage houses, making the entire village a living museum. There are a few open houses and lodging for anyone interested in peeping in. Visitors are asked to respect the privacy of residents in other homes. 

Visiting Shirakawago is a unique cultural experience at any time of the year; however, the best time to visit is during the snow season. 

In January and February, the town hosts Shirakawago Winter Light-Up Festival. When the entire village is illuminated at dusk, the farmhouses covered in snow resemble the gingerbread houses from a winter wonderland.

During the recent festivals, only guests with tickets were permitted to the village to avoid over-tourism and to preserve the cultural heritage. Book your ticket, transportation, and accommodations well in advance to attend the festival. Event details will be announced in the early fall.

Takachiho Gorge 

By Kenny of Knycx Journeying 

Located in a small town in Miyazaki Prefecture, Kyushu, Takachiho Gorge is a lesser-known natural treasure to foreign travelers. It’s long been one of the most popular geological attractions among the locals because of its beautiful scenery and spiritual value. 

The best way to get to Takachiho is self-driving, for travelers on a road trip to Mount Aso, Takachiho Gorge is about 50 kilometers away from the Aso and it takes about one hour to drive there.

It is also possible to visit there by public transportation, as the town has various bus connections with the major cities in Kyushu, like Fukuoka, Kumamoto, and Miyazaki. 

The spectacle is a narrow passage of Gosake River. Both sides of the rocks on the gorge were crafted through a million-year process of volcanic actions.

On top of the 17-meter cliffs are lush and dense green foliage and the Minainotaki waterfall that cascade to the river below, creating a poetic and dreamy picture that leaves visitors in awe. 

There are two ways to appreciate the gorge from different perspectives. From above, take a stroll on the scenic paths on the edge of the cliffs where visitors can have an overview of the entire chasm and the surrounding landscape.

There are a couple of small diners with a table on the terrace and a view of the river. The paths lead to the Takachiho Gorge Boat Rental.

Descend to the surface of the river and row a boat to get into the gorge. Take a closer look at the rock formation and hear the rumbling sound of the waterfall – but be careful that you may get wet if you row right in the falls.  

Noboribetsu Onsen

By Kate of Adventurous Kate

If you want to get off the beaten path in Japan, head to the island of Hokkaido. Want to get even further? Head to Hokkaido in winter. And looking for the ultimate Hokkaido winter gem?

Head straight to the town of Noboribetsu Onsen, a popular spa town in Japan’s northernmost island where the land bubbles with sizzling hot water.

Start your day off with a walk through Jigokudani, or “Hell Valley,” a short walk north of the town center. Here the land is steaming with geothermal activity, tendrils of smoke wafting up from volcanic craters.

Be sure to stick to the wooden walkways, and wear good winter boots if visiting in winter, as there is pretty much always a layer of snow on the ground here!

Next up, get yourself a hearty seafood lunch. The stalls lining the streets are filled with the fresh catch of the day. Settle down for some sushi or grab a chirashi don (bowl of rice with sashimi on top). If you’re visiting in winter, try snow crab or sea urchin.

Finally, it’s onsen time. Onsen Tengoku welcomes day visitors and has plenty of baths of varying temperatures, with a large window overlooking Jigokudani from a distance. You’ll soak away every ache you have from the hike! Be sure to brush up on Japanese spa etiquette before you go.

While Noboribetsu Onsen is a popular spot to overnight or spend the weekend, it also works well as a day trip from Sapporo. Take the train to the town of Noboribetsu (70-100 minutes) and switch to the bus taking you into town (10 minutes).

Magome in the Japanese Alps

By Vicki of Vicki Viaja

If you want to escape to old rural Japan and experience idyllic nature simultaneously, Magome might be the right place for you. The small village in the Japanese Alps is just perfect for those who want to escape the hustle and bustle of the big city of Tokyo for a short time.

Located about a 3-hour drive from Tokyo, Magome can be reached by bus or car.

Magome is also an excellent destination for hikers. As a stop on the Nakasando Trail, a popular approximately 11-day hiking trail through the Japanese Alps, Magome is considered one of the most beautiful places you’ll pass through while hiking.

While (local) hikers may have discovered this peaceful place for themselves, Magome remains pretty much untouched by mass tourism.

The picturesque path that leads through the small village takes you along beautiful old buildings and a few ryokans. Since a few local tour buses frequently come to Magome during the morning hours, it is worth staying overnight to experience the place’s beauty without any tourists.

To complete the experience, it is recommended that you book a ryokan. This way, you will get the complete “Japan experience” in this gorgeous place, with a full typical Japanese dinner and breakfast.

Stroll along the path and discover the sights of the place, such as the cemetery, which offers an incomparable view of the region’s nature.

If you want to experience more of the local nature, you can use the next day to hike on the Nakasendo Trail to the next stop, another cute village called Tsumago. 

The Magome Tsumago Trail is an easy hike that only takes a few hours. If you’re lucky, you may even spot some wildlife along the way, such as Snow Monkeys.

Saiho-ji Temple

JBy ames Ian of Travel Collecting 

Saiho-ji Temple in Kyoto is a small temple in Kyoto that is often called Kokedera “Moss Temple” because of the beautiful moss garden there.  

The site has been a temple since 749, but it wasn’t until 1339 that a garden was added. It was originally a Zen sand garden, but after it fell into neglect about 200 years and flooded, a moss garden grew in its place. 

The garden is centered around a lake shaped like the Japanese kanji symbol for “heart”. There are three tiny islands in the lake called “Sunrise”,  “Sunset” and “Mist”, and a couple of small tea pavilions in between the trees and moss. 

This hidden gem takes some effort to see. The only way to visit is to submit a request for a reservation in writing (snail mail) one week to two months in advance and include a special return postcard for them to mail back to you.

They will designate the day and time and the return postcard then becomes your ticket.  The easiest way to do this is to ask your accommodation provider to help you and use their address.  

On the day of your visit, be sure to bring the confirmation and the fee in cash.  

When you visit, there is a mandatory pre-garden experience at the temple, which may be chanting sutras, meditating, or copying the heart sutra (in kanji).

You are then able to wander the gardens for about an hour. There are over 100 varieties of moss in the gardens, and it is a wonderful, mystical place that few people get to see. 

Nonbei Yokocho

By Catrina of 24 Hours Layover

Nonbei Yokocho – also known as Drunkards Alley is one of the best hidden gems of Japan – located right in the middle of Tokyo would you believe!

Situated out of sight just behind the world’s busiest pedestrian crossing (Shibuya Crossing) you will find this quirky and charming traditional area with several narrow alleyways and lantern-lit streets that feels like a whole new world.

Whilst Shibuya has changed drastically over the years and is now one of the brightest and busiest neighbourhoods in Tokyo, it’s amazing how you can still find a small reminder of the old town amongst the back streets.

Nonbei Yokocho is definitely a lovely place to escape the crowds for the lucky few who know about this unique little spot. There are many little restaurants and bars here – some so small that they can only hold around 4 people at once!

They are filled with local people and these ‘yokocho’ (alleyways) in Tokyo are definitely worth a visit, if not to experience the true Tokyo, then at least to have a break from the crowds and experience one of the most hidden yet authentic photo spots in Tokyo.

The bars are restaurants have been here in Nonbei Yokocho since the 1950’s – before then this was home to the Tokyu railway corporation Head Office.

Nonbei Yokocho is probably the most authentic ‘yokocho’ in Tokyo you’ll find. It’s full of character and is an absolute must-visit when you’re here, making it one of the best secret spots in Japan.

Travel tip: head here in the evening so you can go inside the small bars for a drink and to mix with the locals! Each of the bars have their own unique atmosphere and are very cosy! Note that most of the bars are shut on Sundays and during the day!