Hidden Gems to Visit in Japan
“How can I avoid tourists in Japan?”
That’s a bold question!
But I get it. Someone really asked us this. Someone other than Aki & me, who also ask this question sometimes as we’re out and about (around Osaka and Kyoto in particular).
You’re not coming to Japan to be surrounded by tourists, doing touristy things, in some kind of fantasyland theme-park version of the universe. No no, that’s not you. You want the real deal.
Fair enough. That’s what we want for you, too!
While iconic destinations like Tokyo's Shibuya Crossing and Kyoto's Fushimi Inari Shrine deserve their fame, the true essence often lies in Japan’s hidden gems — in its lesser-known corners. So to that end, we've curated a journey through Japan's hidden gems and secret places to visit. These are areas and spots that yield authentic experiences away from the well-trodden tourist paths, and they’re ideal for senior tours, honeymoons and more.
Kansai/Kinki Region: Hidden Gems Beyond the Tourist Sites of Kyoto & Osaka
Kyoto, the cultural heart of Japan, is famous and popular around the world for its Shinto shrines, Buddhist temples & Japanese gardens. However, venture beyond the city limits, and you'll discover a Kansai region brimming with unexpected treasures.
For this article, we’re giving you one Kyoto gem, nearby Uji; followed by three hidden gems within driving distance up on the Japan sea coast.
Uji: A Tea Lover's Paradise Near Kyoto That Was a Hidden Gem (Still a Gem!)
Just a short train ride from Kyoto lies Uji, a small city that's the cradle of Japanese green tea.
While many visitors make a quick stop at the famous Byodo-in Temple, true hidden gems await those who linger. If you get to the temple before it opens, you can explore the grounds slowly, catching the morning light on the pond that reflects this magnificent Buddhist temple.
If it looks familiar, like you’ve somehow been here before, take out a 10-yen coin. Yup, that’s Byodo-in on the back of the coin! You’ll see many visitors holding up a coin with the pond and temple in the background, a now-classic photo op. But wait, there’s more! Yes, more money for you! If you happen to have a 10000-yen bill, look at the phoenix on the back, then glance at the phoenix on top of the structure. That’s right, Byodo-in is on not one but two pieces of Japanese currency.
Afterwards, you’ll see a Starbucks across the street. No bonus points for you if you drink a coffee here! Nothing against Starbucks, but you’re in Japan’s tea capital!
Instead, why not explore the Taiho-an tea house, where you can participate in an authentic tea ceremony surrounded by meticulously manicured gardens.
Speaking of teahouses, would you like to have lunch or dessert at the oldest one in the world? Yeah, thought you might. It’s called Tsuen, and this teahouse is located just over the bridge from the main street in Uji (across the street from the Keihan train station). We enjoyed a nishin soba (cold noodle dish with herring on top), a seasonal treat in the summer – and, bonus, the soba noodles are made with matcha green tea!
While we had to wait over 30 minutes on a weekday to get in for a late lunch, it was well worth it. But it also speaks to the rise in popularity of Uji, so let’s say it’s no longer a “hidden” gem, but still a gem that many can enjoy.
For a unique experience, visit one of the local tea farms during harvest season (April to October) and try your hand at picking tea leaves alongside farmers whose families have cultivated this land for generations.
The Japan Sea Coast: Kyoto, Hyogo & Tottori Prefectures
If you’ve rented a car (on a roundtrip from Osaka, Kyoto or Kobe), you can make a loop drive that combines three nice destinations on the Japan sea coast: Funaya, Kinosaki Onsen and the Tottori Sand Dunes.
Ine no Funaya: Northern Kyoto Prefecture’s Fishing Village
On the northern coast of Kyoto Prefecture, the fishing village of Ine offers a glimpse into a way of life that has remained largely unchanged for centuries.
The village's unique "funaya" boat houses – wooden structures built on stilts over the water – create a picturesque scene often likened to Venice (if you must). Take a leisurely boat tour around the bay, chat with friendly locals and sample the day's catch at a family-run restaurant.
As the sun sets, the reflection of the funaya on the calm waters creates a magical atmosphere that few visitors to Japan ever experience.
Kinosaki Onsen: Soaking It All In on the Sea of Japan Coast
Nestled in the northern part of Hyogo Prefecture, Kinosaki Onsen offers a glimpse into Japan's enduring love for hot springs, all while maintaining an atmosphere of historic charm that feels worlds away from the country's modern cities.
Seven Public Baths, One Unforgettable Experience
What sets Kinosaki apart from other onsen towns is its unique bathing culture. Instead of being confined to your ryokan's baths, visitors are encouraged to partake in the time-honored tradition of sotoyu meguri, or bath hopping. Put on your yukata (basically like a lightweight cotton kimono) and geta (wooden sandals), and stroll along the willow-lined canals to visit all seven of the town's public bathhouses.
Each bathhouse has its own character and is said to have unique healing properties. Satono-yu, the largest, features a cave-like atmosphere with baths made of natural rocks, while Jizo-yu is said to be particularly beneficial for fertility and safe childbirth. Visiting all seven is believed to bring good fortune.
Got a tattoo? No worries! Unlike many other onsen in Japan, Kinosaki Onsen is tattoo friendly!
Seasonal Delights: What to Eat in Kinosaki Onsen
Each season brings its own charm to Kinosaki Onsen. Spring sees the canal banks burst into pink with cherry blossoms, while autumn turns the surrounding mountains into a sea of reds, oranges and yellows. Winter, however, might be the most magical time to visit. The town often receives a dusting of snow, creating a scene straight out of a woodblock print. It's also the best season to savor Matsuba crab, a local delicacy caught in the nearby Sea of Japan.
A visit to Kinosaki Onsen lets you experience Japanese bathing culture, giving you a chance to know a way of life that has remained largely unchanged for centuries. Oh, and it’s a great spot for honeymooners in Japan, too!
Tottori Sand Dunes: Japan's Unexpected Desert Coast
When most people imagine Japan, sand dunes are probably not the first thing that comes to mind. Yet, along the Sea of Japan coast in Tottori Prefecture lies a natural wonder that seems transported from another continent entirely: the Tottori Sand Dunes.
A Hidden Gem in the Sand? Yes, Japan’s Got That!
Stretching for 16 kilometers along the coast and reaching up to 50 meters in height, the Tottori Sand Dunes are the largest in Japan. Formed over thousands of years by sand carried from the nearby Sendai River and shaped by coastal winds, these dunes offer a striking contrast to the lush greenery typically associated with Japan.
Walking among the dunes, you might feel as though you've been transported to the Sahara. The constantly shifting sands create an ever-changing landscape of ripples and patterns, particularly beautiful at sunrise and sunset when long shadows accentuate the dunes' contours.
Desert Adventures in Tottori on the Japan Sea Coast
Despite their relatively small size compared to the world's great deserts, the Tottori Sand Dunes offer plenty of activities for adventure seekers. Try sandboarding down the slopes, or for a truly unique experience, take a camel ride along the dunes' edge. For a bird's-eye view, paragliding services offer flights over the dunes and the adjacent Sea of Japan.
The Tottori Sand Museum, located near the dunes, hosts impressive sand sculptures crafted by artists from around the world. The exhibits change annually, each focusing on a different country or theme.
After a day of desert exploration, sample some local specialties. Tottori is famous for its Matsuba crab, similar to that found in Kinosaki. The prefecture is also one of Japan's largest producers of nashi (Asian pears), known for their crisp texture and sweet flavor.
The Tottori Sand Dunes offer a side of Japan that few tourists ever see. Why not experience the warmth and hospitality of a region that remains largely off the international tourist radar?!
Nagoya: The Unsung Hero of Central Japan
Often overlooked in favor of its more famous neighbors, Nagoya holds its own as a city of industry & innovation, history and some of Japan’s best comfort food.
Toyota Commemorative Museum of Industry and Technology
While not an entirely hidden gem, this museum is frequently missed by international visitors. Housed in the original red-brick factory where Toyota began as a textile machinery company, the museum offers a fascinating look atJapan's industrial revolution. Enjoy a hands-on exploration of the ingenuity that propelled Japan to the forefront of global manufacturing.
Oasis 21 and TV Tower: A Futuristic Oasis
For a taste of modern Japan, head to Oasis 21, a multi-level complex topped by the "Spaceship Aqua" – a water-filled glass roof that offers a unique walking experience and pretty cool views of Nagoya TV Tower. At night, the illuminated complex becomes a gathering spot for locals, with occasional events and performances adding to the vibrant atmosphere. It's a great place to experience Nagoya's contemporary culture largely away from the tourist crowds.
Nagoya: Japan’s Soul Food That’s a Hidden Gem of Its Own
While Kyoto is famous for kaiseki and Tokyo has more Michelin-starred restaurants than any city in the world, Nagoya is home to Japan’s version of “soul food.”
Here you can enjoy comfort foods like miso katsu, a fried pork cutlet in a tangy miso sauce – and Yabaton is the place where you want this.
Other Nagoya favorites include kishimen (an udon-like noodle soup); miso nikomi udon (if you kinda want to mix the two previous dishes!); hitsumabushi (chopped eel on rice); pub food like Yamachan’s famous fried, spiced chicken wings; and Taiwan ramen.
Just the other day, I saw a photo of something called “an-kake spaghetti,” which is a play on an-kake udon but using pasta – and then they added karaage fried chicken on top! Apparently it’s becoming more popular in Nagoya these days, and that tells you a lot about this hidden gem (hiding in plain sight!) of a Japanese city renowned for its comfort food.
Curious? You can learn more in our Nagoya city guide.
Tohoku: Hidden Gems in Japan’s Vast North
The Tohoku region, comprising the northeastern part of Honshu, is a treasure trove of natural beauty, ancient ways and warm hospitality. These hidden gems and secret places of Japan’s north await you.
Still recovering from the 2011 earthquake and tsunami, this hidden gem in Japan welcomes visitors with open arms, offering experiences that harken back to an older version of Japan (and refreshingly so, in the best ways possible).
Ouchi-juku: A Living Edo-Period Village
Step back in time in Ouchi-juku, a former post town in Fukushima Prefecture that looks almost exactly as it did during the Edo period. Talk about Japan’s hidden gems!
The village's thatched-roof houses line an old road once used by samurai traveling between Edo (Tokyo) and Aizu. Wander the car-free streets; sample local delicacies like negi-soba (buckwheat noodles eaten with a whole green onion in lieu of chopsticks); and stay overnight in a traditional minshuku (guesthouse) for a local, immersive experience and a true hidden gem of Japan.
Sanriku Coast: Rebirth & Natural Wonder
The rugged Sanriku Coast in Iwate Prefecture offers both natural beauty and a poignant look at recovery efforts following the 2011 tsunami.
Visit the Kitayamazaki Cliffs for ocean vistas and hidden places in Japan, then take a boat tour through the dramatic rock formations of the Jodogahama Beach area. In nearby Rikuzentakata, witness the miracle of the "Miracle Pine" – the sole tree to survive the tsunami out of 70,000 in a coastal forest, now preserved as a memorial. The area's recovery and the resilience of its people offer a profound and often overlooked aspect of contemporary hidden gems in Japan.
Nyuto Onsen: Hot Springs Hidden in the Hills
Hidden deep in the mountains of Akita Prefecture and among this regions hidden gems to visit in Japan, Nyuto Onsen is a collection of seven traditional hot spring ryokan, each with its own unique mineral composition and healing properties.
The most famous, Tsurunoyu, dates back over 300 years and offers mixed-gender outdoor baths surrounded by pristine forest. Soak in milky white waters as snow falls gently around you in winter, or listen to the symphony of cicadas in summer. Enjoy this experience of total immersion in nature that feels worlds away from modern Japan.
Tokyo's Hidden Corners: Urban Exploration Off the Beaten Path
Even in Tokyo, a city that seems to have been explored from every angle, Japan’s hidden gems await the curious traveler willing to venture beyond the guidebooks.
Yanaka: A Village in the City
While the nearby Ueno Park draws crowds, the Yanaka district offers a peaceful glimpse into old city life as a hidden gem in Tokyo.
Wander through narrow streets lined with historic wooden houses, artisan workshops and small temples. The Yanaka Cemetery, with its cherry blossom-lined paths, offers a calm respite (a true hidden gem) from Tokyo’s famous organized chaos, hustle & bustle. Kagyozaka is a steep stone staircase that featured in Natsume Soseki's novel "Sanshiro" – it's a favorite spot for photographers seeking to capture the essence of old Tokyo.
Yanaka Ginza is a highlight for many visitors. This shotengai or shopping street shows a great example of daily, local life in Japan. Stroll up and down its lanes. Check out the fruits and vegetables on display, as well as the meat and seafood. Duck into a kissaten cafe for a cup of coffee or slice of cake. Chat up one of the merchants as you get take-out food for your dinner tonight or breakfast the next day.
Unlike tourist trap Tsukiji, a shotengai like Yanaka Ginza (and there are many good ones in and around Tokyo) is a must visit if you’re looking for hidden gems in Japan.
Todoroki Valley: Urban Oasis in Tokyo Prefecture
A short train ride from Shibuya lies Todoroki Valley, a Tokyo hidden gem as its only ravine and a tucked away natural paradise. A wooden path meanders alongside a gentle stream, passing by moss-covered stones, bamboo groves and small shrines. The chirping of birds and the burbling of the stream make it hard to believe you're still in the city limits in the world's largest metropolis. End your walk at the charming Setsugekka tea house, where you can enjoy matcha and wagashi (Japanese sweets with a long history) while overlooking the valley.
Embracing the Hidden Gems on Your Japan Itinerary
These hidden gems and secret places to visit in Japan offer a glimpse of the depth and diversity of experiences waiting to be discovered here.
By venturing beyond the familiar, you’re opening up to encounters that reveal the true heart of this fascinating country – in its small towns, local festivals, family-run ryokan and most importantly, in the genuine interactions with people who want to share their culture and traditions.
Want to talk about adding hidden gems in Japan to a customized travel itinerary? Why not schedule your FREE consultation, using the link below:
FAQ - Frequently Asked Questions About Hidden Gems in Japan
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While Japan's major cities are well-connected by bullet trains, reaching hidden gems often requires a combination of local trains, buses, and sometimes rental cars. The Japan Rail Pass used to be great for cost-effective travel; though recent price hikes of that pass make point-to-point tickets a better option in many cases.
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Absolutely! Japan is generally very safe for solo travelers. Many of these hidden gems offer a chance to connect with locals and other travelers in a more intimate setting than you'd find in major tourist areas. However, in very rural areas, some basic Japanese language skills can be helpful.
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The best time depends on your preferences and the specific regions you're visiting. Generally, spring (March to May) and autumn (September to November) offer pleasant weather and beautiful scenery across most of Japan. However, for some hidden gems:
Tohoku has a popular cherry blossom (sakura) season in April, as well as beautiful fall colors (Oct-Nov)
Kinosaki Onsen's hot springs are particularly magical in winter, especially when surrounded by snow
Summers have a rainy season (early June to Mid-July) followed by high heat & humidity (into September)
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While dietary restrictions can be challenging in rural Japan, it's becoming easier. Many ryokan and small restaurants are willing to accommodate if given advance notice. Learn some key phrases to explain your needs, and consider carrying a dietary restriction card in Japanese. In larger towns, you may find restaurants catering to various dietary needs, but it's always best to plan ahead and communicate your requirements clearly. Got questions? Let us know, we're always happy to help!