Off the Beaten Path Japan: 15 Secret Hidden Gems to Explore

As the country epitomizing the myriad fascinations of the travel industry, Japan has to offer more than the glowing signs and the fast-paced rhythm of modern life, along with the temples and the tranquil lifestyle of old Japan, or the extravagant street kiosks and the constant rush of Osaka. However, within the borders of the country, there is more to offer, with more than enough contrast to the metropolitan areas. This is a country unlike any other, and it knows the importance of rest. Traditional towns, ancient onsen, and picturesque towns just waiting to be hiked and explored. For the best-kept secrets of exploring Japan, it is an endless journey.

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Why Explore Japan’s Hidden Gems?

For any place, there is more than just the view. The best-kept secrets in Japan offer traditional Japanese hospitality and warmth, and still manage to remain largely untouched. Exploring these secrets means the opportunity to view the assimilation of the culture of forgotten towns, along with the bundles of hospitality waiting to be discovered. Exploring the culture of these towns largely showcases the value of the region.

15 Secret Places in Japan Worth Exploring

Kumano Kodo (Wakayama) – Ancient Pilgrimage Trails

The Kumano Kodo in Wakayama is one of Japan’s most spiritual journeys. These sacred trails, dating back over a thousand years, once welcomed emperors and pilgrims seeking enlightenment. Today, walking the forested paths, crossing mossy bridges, and visiting hidden shrines feels like stepping into another era. Unlike crowded attractions, this off-the-beaten-path Japan travel experience offers peace, history, and cultural depth in equal measure.

Ine no Funaya (Kyoto) – Boathouses on the Water

In Kyoto’s coastal town of Ine, rows of traditional wooden boathouses known as funaya stand gracefully along the bay. These unique structures are built directly on the water, with boats tucked beneath the living quarters. Visiting Ine no Funaya offers a glimpse into a secret village in Japan where fishing traditions remain unchanged for centuries. The slow pace, fresh seafood, and scenic views make it one of Japan’s hidden gems for travelers seeking authentic charm.

Shirakawa-go (Gifu) – Thatched-Roof Village

Shirakawa-go is located in the Japanese Alps and is recognized for its traditional thatched-roof houses. In the winter season, the picturesque village is transformed into a winter wonderland, and in the summer, it features beautiful fields and mountain views. As a UNESCO World Heritage Site, the village is a quiet reminder of the enchanting rural life that is mostly lost. It is a unique destination in Japan, allowing visitors to explore the farming and rural architectural ingenuity.

Ouchi-juku (Fukushima) – Edo-Period Post Town

Ouchi-juku is a perfectly preserved post town that served as a rest stop for travelers along the Aizu-Nishi Kaido trade route. It features thatched-roof houses, narrow streets, and soba noodles shop pillars, giving Japan a 19th-century feel. With its unique and historical charm, it is a hidden and authentic destination, combining the rich allure of history, which is often overlooked by many tourists.

Lake Kussharo (Hokkaido) – Frozen Lake and Hot Springs

Hokkaido conceals many natural wonders, and Lake Kussharo is one of a kind for its unique combination of frosty beauty and hot spring wonders. In the winter, swans flock around the waters, which is a delightful sight. In the summer, the area turns into greenery, perfect for hiking and canoeing. This is one of the many remote places to visit in Japan, and it is a perfect juxtaposition of nature.

Hoshinoya Fuji (Yamanashi) – Luxury Glamping with Mt. Fuji Views

Having a unique combination of comfort and adventure, Hoshinoya Fuji is the place one must visit to have the prestigious glamping experience overlooking Mt Fuji. This hidden glamping site is located in the forest above Lake Kawaguchi, perfectly located in nature. Having a perfect sight of Mt Fuji is one thing, but having your own cabin and a perfect night of staring at the stars is bliss. This is a perfect spot for luxury lovers and nature advocates.

Benesse House (Naoshima Island) – Art Meets Hospitality

Naoshima Island is famously known as “Japan’s art island,” and Benesse House elevates the experience even further by merging a contemporary art museum and a hotel. Visitors sleep beside world-class art, walk through outdoor installations, and enjoy views of the Seto Inland Sea. For those looking for unusual, non-touristy spots in Japan, this location offers a perfect combination of creativity, culture, and hospitality.

Ganso Daruma (Osaka) – Kushikatsu Heaven

Aside from takoyaki and okonomiyaki, Osaka’s other hidden culinary treasures are kushikatsu – deep-fried meat and vegetable skewers. Ganso Daruma, located away from the busiest streets of the city, is the origin of this beloved dish. Eating here and connecting with the city’s authentic food culture is a unique experience, as some of Japan’s hidden treasures are not just in the beautiful landscapes but also in the food.

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Kanazawa Omi-cho Market – Fresh Crab and Sushi

Even though it’s not as famous as Kyoto or Tokyo, Kanazawa’s Omi-cho Market is a great place to get regional seafood. For example, this lively place specializes in snow crabs and also serves oysters, sushi, and other regional specialties. This relatively hidden part of the country is a great destination, as the combination of food, history, and hospitality makes for a remarkable and memorable journey.

Okonomimura (Hiroshima) – Okonomiyaki Wonderland

Hiroshima is famous for its layered savory pancake, okonomiyaki, which is also made with noodles. People who visit Okonomimura get to sample the many different variations of the dish from different local chefs. This multi-storey building, which is dedicated to the making of okonomiyaki, serves as a culinary paradise for tourists. Okonomimura is an underappreciated attraction as it showcases not only Hiroshima’s creativity in the kitchen, but also its resilience as a city.

Nakano Broadway (Tokyo) – Retro Anime Paradise

For enthusiasts of anime and manga, Nakano Broadway is a unique place to shop in Tokyo. This is because, unlike Akihabara’s commercialized shopping, the old shopping complex presents a nostalgic atmosphere. There is a thriving otaku culture located within the old shopping complex, as the place is stocked with rare vintage figures and nostalgic collectibles. Even casual shoppers, who are not interested in the otaku culture, will be interested in seeing this unique side of Tokyo.

Shinsaibashi-suji (Osaka) – Local Arcade Shopping

Shinsaibashi-suji is Osaka’s historic shopping arcade, where traditional stores mix with trendy boutiques. Unlike department stores, this lively arcade offers an authentic look at how locals shop, eat, and socialize. It’s a hidden gem in Japan that blends history with modern life, offering visitors both souvenirs and cultural immersion.

Hakone Tozan Railway: An Old, Scenic Railway

Hakone Tozan Railway is the oldest train service of the Hakone Tozan Railway. It’s also one of the most picturesque train rides. The train also offers zig-zag rides on the mountain, where you get amazing views, picture-laden forests, and breathtaking landscapes from the passes, tunnels, and bridges. This is an experience of the un beaten path of Japan, and proves the adage that sometimes, the journey is much more fulfilling than the destination.

Kyoto Machiya Taxi – An Additional Layer of Cultural Exploration

Although Kyoto is most historic and famous because of its temples and geisha districts, an additional layer of hidden cultural exploration can be done using Machiya Taxis. These are Kyoto-styled taxis, which are designed like Kyoto townhouses, and are driven by guides who share pieces of the city’s cultural stories. This is one of the most intimate and hidden ways of observing and navigating one of the most historic cities in Japan.

Ginzan Onsen (Yamagata) – Magnificent Winter Destination

The highlight in this onsen town is the winter season. It is the most magical winter onsen town, romantically and traditionally. It offers a picturesque backdrop of the town, just like in a fairy tale. You get the winter backdrop of glowing lanterns in the town, and the steaming baths invite the onsen town. It offers romance and tradition.

Advice on Visiting Japan's Hidden Gems

Deciding when to explore Japan’s less frequented places takes planning. This depends on your destination you could explore Ginzan Onsen in winter to enjoy its idyllic winter setting, the Kumano Kodo for autumn hiking, or visit Shirakawa-go in spring to see the cherry blossoms. Visiting less popular towns off the beaten track may prove difficult. This is why it may be best to get a regional pass or rent a car to give you the best flexibility. Economically, less popular towns and cities in Japan are far cheaper than Tokyo or Kyoto, making them great for an extended visit.

Appreciating and respecting the local culture is crucial. Many of these off-the-beaten-track places in Japan are small communities where age-old traditions are the norm. Simple gestures like learning a few local greetings, supporting locals, and observing local etiquette when in these places can go a long way in preserving the charm and authenticity of these destinations.

What are the hidden gems in Japan?

This can be off the beaten path villages, lesser known towns, unique attractions, and places where tourists are few, like Shirakawa-go, Ouchi-juku, Ine no Funaya, and Ginzan Onsen.

Which is the most underrated city in Japan?

Most people consider Kanazawa to be the most underrated city in Japan, as it has a samurai district, lovely gardens, and a bustling seafood market, all without the crowds.

Where are Japan’s secret villages?

Japan’s secret villages include Shirakawa-go (Gifu), Ine no Funaya (Kyoto), and Ouchi-juku (Fukushima), all of which retain historical architectural and cultural practices.

What is the best off-the-beaten-path place in Japan?

The Kumano Kodo pilgrimage trails in Wakayama are the best off-the-beaten-path places in Japan, where one can experience a blend of history, spirituality, and natural surroundings.

Is Japan safe to explore remote areas?

Yes, Japan is very safe in terms of exploring remote areas, keeping in mind to have transportation planned and to have the proper researched local conditions, particularly in the mountains.

What is the most unique hidden onsen town in Japan?

Yamagata’s Ginzan Onsen is considered the most unique hidden onsen town, characterized by its wooden lodges, the snowy atmosphere, and historic sensibilities.