Katie and Pierce
When most people think about visiting Japan, they picture Tokyo’s bright lights, Kyoto’s temples, or Osaka’s amazing food. While these cities are incredible, Japan has so many more special places waiting for you. These hidden gems in Japan give you a chance to see the real country, away from the busy tourist crowds.
From volcanic islands to ancient temples, traditional villages to natural hot springs, these hidden gems in Japan will show you sides of the country that most travelers never get to see. Pack your bags and get ready for an adventure!
1. Iya Valley, Tokushima Prefecture
Tucked away in the mountains of Tokushima, Iya Valley feels like stepping into another world. This remote area is famous for its scary but exciting vine bridges that hang high above rushing rivers. The valley is filled with steep cliffs, traditional thatched roof houses, and some of the most beautiful mountain views in Japan.
The vine bridges were originally built by ancient warriors as escape routes, but today they give visitors an unforgettable thrill. Walking across these swaying bridges definitely gets your heart pumping! The valley is also perfect for hiking and soaking in hot springs while surrounded by nature.
2. Mashiko, Tochigi
Art lovers will fall head over heels for Mashiko, one of the most creative hidden gems in Japan. This charming town has been making pottery since the 1800s. With around 250 kilns and 50 galleries scattered throughout the area, this place is a paradise for anyone who loves handmade crafts.
The local pottery style uses iron-rich clay that makes pieces feel substantial and sturdy. You’ll see beautiful bowls, cups, and plates with simple painted designs that look both traditional and modern. Visit during one of the twice-yearly pottery fairs to see amazing work and maybe score some great deals when shops bring their pieces outside.
3. Aogashima Island, Tokyo
Yes, this volcanic island technically belongs to Tokyo, but it’s about as far from the city’s chaos as you can get. Aogashima sits in the Philippine Sea and is home to only about 160 people, making it one of Japan’s most remote inhabited islands.
The entire island is actually a volcano, and you can hike around the crater rim for incredible views. At night, the lack of light pollution makes this one of the best stargazing spots in all of Japan. There are also natural hot springs heated by volcanic activity where you can relax after a day of hiking.
4. Tono, Iwate
Hidden in the mountains of northern Japan, Tono has a secret that beer lovers will appreciate: it grows about one-sixth of all the hops used in Japanese beer! This is truly one of the most unexpected hidden gems in Japan. The area’s climate creates perfect conditions for hop farming, and local breweries have taken full advantage.
You can bike through rolling hop fields and end up at cozy taprooms like Tono Brewing or jazz bar Brew Note Tono. The scenery is beautiful, with mountain views and even an old steam locomotive track running through the valley. It’s the perfect place to combine outdoor activities with craft beer tasting.
5. Nachi Falls, Wakayama Prefecture
At 436 feet tall, Nachi Falls is one of Japan’s most spectacular waterfalls. But this isn’t just about the impressive height; the waterfall is considered sacred and sits next to the beautiful Seigantoji Temple, creating a spiritual atmosphere that’s hard to find anywhere else.
The combination of rushing water, ancient temple buildings, and surrounding forest makes this place feel magical. Many visitors say they feel a sense of peace and wonder standing before the falls. The temple has been here for over 1,000 years, so you’re experiencing something that has inspired people for generations.
6. Goto Islands, Nagasaki
These islands off the coast of Kyushu have some of Japan’s most beautiful beaches, but without the crowds you’ll find in Okinawa. The Goto Islands are among the lesser-known hidden gems in Japan that offer white sand beaches meeting crystal clear water, with fishing villages dotting the coastline like something from a postcard.
The islands also have a fascinating hidden history. During Japan’s ban on Christianity, many believers fled here and practiced their faith in secret for over 200 years. You can visit small chapels and learn about how these communities survived by disguising their religious practices. Plus, the local udon noodles are absolutely delicious.
7. Koyasan, Wakayama Prefecture
Mount Koya is the heart of Shingon Buddhism and home to over 100 temples. This mountaintop religious center has been welcoming pilgrims for more than 1,200 years, and today you can experience temple life firsthand.
Stay overnight in a temple lodging called shukubo, where you’ll eat vegetarian meals, join morning prayers, and sleep in traditional rooms. It’s a chance to slow down and experience a completely different way of life. The morning mist rolling through the cedar trees and the sound of temple bells create an atmosphere you’ll never forget.
8. Akita Prefecture
Choosing just one place to visit in Akita Prefecture is tough because each season brings something special. Spring brings weeping cherry blossoms over preserved samurai houses in Kakunodate. Summer features the amazing Kanto Festival where people balance huge bamboo poles covered in lanterns.
Fall turns the hot springs area of Nyuto Onsenkyo into a wonderland of red maple leaves. Winter might be the most exciting time of all, with unique festivals including people dressed as demons to scare children into good behavior. No matter when you visit, Akita will surprise you.
9. Shirakawa-go, Gifu Prefecture
This village looks like it came straight out of a fairy tale. The traditional farmhouses have incredibly steep thatched roofs designed to handle heavy snow, and the whole village sits in a beautiful mountain valley.
Winter is the most magical time to visit when snow blankets everything in white. The houses look like gingerbread cottages, and the village feels completely peaceful. You can stay overnight in one of these traditional houses and experience what life was like centuries ago, complete with hearth fires and home-cooked meals.
10. Nanjo, Okinawa
While most people head to Okinawa’s famous beaches, Nanjo on the southern coast has attractions that connect you with the island’s spiritual side. The Valley of Gangala features ancient limestone caves with massive banyan trees that locals believe house sacred spirits.
Nearby Sefu-Utaki is a place where Okinawan priestesses were once inducted into religious service. Between these two spiritual spots sits tiny Ojima island, famous as the birthplace of Okinawan-style tempura. Stop by family-run shops like Oshiro Tempura for seaweed fritters served hot and crispy.
11. Kurashiki, Okayama Prefecture
Step back in time in Kurashiki’s Bikan Historical District, where Edo-period storehouses line peaceful canals. White-walled buildings reflect in the water while willow trees create natural archways overhead. The whole area has been so perfectly preserved that you might feel like you’re walking through a movie set.
Take a boat ride with a traditionally dressed guide who’ll punt you along the canals while sharing stories about the area’s history as a rice distribution center. The district also has great museums, art galleries, and restaurants housed in these historic buildings.
12. Tsuruoka, Yamagata
Tsuruoka might seem like an unusual destination, but it has one of Japan’s most mesmerizing attractions: the Kamo Aquarium, which specializes in jellyfish. Massive illuminated tanks full of colorful, pulsating jellyfish create an otherworldly experience that’s surprisingly relaxing to watch.
The nearby sacred mountains of Dewa Sanzan add a spiritual element to your visit. These three peaks are holy to followers of Shugendo, an ancient mountain religion. Misty temples and hiking trails through old-growth forests make this area feel mystical and untouched by modern life.
13. Kawagoe, Saitama Prefecture
Known as “Little Edo,” Kawagoe is like having a time machine just a short train ride from Tokyo. The town has kept its Edo-period atmosphere with well-preserved streets, traditional warehouses, and sweet shops that have been family-run for generations.
The bell tower that rings throughout the day has been marking time for centuries, and the narrow streets are perfect for wandering. You can try traditional sweets, shop for crafts, and experience what Tokyo might have felt like hundreds of years ago, all without dealing with big city crowds.
14. Oki Islands, Shimane
This cluster of islands off Shimane’s coast are known for their incredible natural beauty. The Oki Islands rank among Japan’s most spectacular hidden gems in Japan with steep cliffs topped with green fields where wild horses roam free, ocean caves where bioluminescent plankton light up the water like blue stars, and ancient cedar trees create an almost magical landscape.
The small fishing villages scattered across the islands welcome visitors warmly. Local izakaya pubs serve incredibly fresh rock oysters and turban shells paired with sake from the hometown Oki Sake Brewery. With only a few thousand residents total, these islands feel like a well-kept secret.
15. Kiso Valley, Nagano Prefecture
The ancient Nakasendo Trail once connected Kyoto with Edo (now Tokyo), and some of the best-preserved sections run through the beautiful Kiso Valley. Walking this historic route, especially between the post towns of Magome and Tsumago, gives you a real sense of what travel was like during Japan’s feudal period.
These old post towns have been lovingly maintained with traditional inns, tea houses, and shops that look much like they did centuries ago. The trail itself winds through forests and mountains, making it a perfect combination of history, culture, and natural beauty.
16. Gunkanjima (Battleship Island), Nagasaki Prefecture
This abandoned island has one of the most haunting and fascinating stories in Japan. Once home to a thriving coal mining community, Gunkanjima was completely abandoned when the mine closed, leaving behind concrete apartment buildings and industrial structures that nature is slowly reclaiming.
The island gets its nickname from its shape, which looks like a battleship when viewed from the water. Guided tours let you walk through the ruins and learn about Japan’s industrial past while seeing how quickly nature takes back abandoned places. It’s eerie, beautiful, and unforgettable all at once.
17. Ise-Shima National Park
This scenic national park is dotted with islands and known as the birthplace of pearl cultivation. The sheltered bays still have floating pearl farms where oysters dangle from ropes, keeping the water crystal clear. Remote fishing villages continue the traditional practice of pearl farming that started here.
The park is also home to luxury resorts like Cova Kakuda, which was built in a renovated pearl processing station. With only four villas, it focuses on sustainability with onsite farming and fresh seafood sourced directly from local fishing families. It’s a perfect place to experience Japan’s connection to the sea.
18. Yakushima, Kagoshima Prefecture
This subtropical island inspired the forest scenes in the Studio Ghibli film Princess Mononoke, and once you see it, you’ll understand why. Ancient cedar trees, some over 1,000 years old, create a primeval forest that feels like stepping into a fantasy world.
The island is a hiker’s paradise with trails leading through moss-covered forests where unique wildlife lives. The combination of subtropical climate and ancient trees creates an ecosystem unlike anywhere else in Japan. Rain is common, but it just adds to the mystical atmosphere of this green wonderland.
19. Tottori Sand Dunes, Tottori Prefecture
Japan’s only large sand dunes stretch along the coast and create a landscape that looks more like the Sahara than traditional Japan. The Tottori Sand Dunes are definitely one of the most unique hidden gems in Japan. These massive dunes shift and change with the wind, creating new patterns and shapes constantly.
You can try sandboarding down the steep slopes or even take a camel ride for a truly unique Japanese experience. The contrast between the golden sand and the blue Sea of Japan creates stunning photo opportunities, especially at sunrise and sunset when the light makes the dunes glow.
20. Amanohashidate, Kyoto Prefecture
Known as the “bridge to heaven,” this natural sandbar stretches across Miyazu Bay and is considered one of Japan’s three most scenic views. The pine-covered strip of land creates a bridge-like formation that’s been inspiring artists and poets for over 1,000 years.
You can walk or bike across the entire sandbar, stopping at small shrines and enjoying views of the bay from both sides. The traditional way to view Amanohashidate is to bend over and look at it upside down between your legs, which supposedly makes it look like a dragon flying across the sky.
21. Nagato Yumoto, Yamaguchi
This rural hot spring town shows what happens when a community works together to preserve and improve their home. Nagato Yumoto represents one of the most welcoming hidden gems in Japan. The 600-year-old Onto hot spring got a beautiful new bathhouse design, and the Otozure River running through town has well-maintained walking paths and piers.
Local restaurants serve regional specialties like kawara soba, where tea-infused noodles and beef are cooked on ceramic rooftiles. The town’s fifth-generation ryokan owners lead revitalization efforts, making this a great example of how traditional Japanese hospitality continues to evolve while honoring the past.
