Discover Japan’s Hidden Charms: 4 Secondary Cities to Visit This May

May is the perfect time to explore Japan—mild weather, blooming flowers, and a peaceful atmosphere before the summer crowds roll in. It’s an ideal season for travelers looking to experience a different side of Japan, away from the usual tourist hotspots.

While cities like Tokyo, Osaka, and Kyoto steal the spotlight, Japan’s secondary cities hold their own unique charm. These underrated cities in Japan offer stunning landscapes, rich cultural heritage, and incredible local cuisine—without the hustle and bustle of major tourist hubs.

This May, step off the beaten path and uncover the beauty of four hidden gem cities in Japan. Whether you’re drawn to history, nature, or authentic local experiences, these destinations promise an unforgettable journey. Let’s explore Japan’s secondary cities together with Gother!

Among Japan’s underrated cities, Gifu is a hidden treasure waiting to be explored. Located in central Japan, just two hours from Tokyo by Shinkansen, this picturesque prefecture is known for its stunning mountain landscapes, historic villages, and deep-rooted cultural heritage.

May is the perfect time to visit, as the cool, fresh air enhances the charm of its scenic countryside. With a mix of breathtaking nature and centuries-old traditions, Gifu stands out as one of Japan’s secondary cities that offers an authentic and peaceful travel experience beyond the usual tourist paths.  
 

Shirakawa-go (Shirakawa Village)

For those fascinated by traditional architecture and authentic rural life, Shirakawa-go is a must-visit. Recognized as a UNESCO World Heritage site, this historic village is famous for its Gassho-zukuri houses—steep thatched-roof homes designed to withstand heavy snowfall in winter.

May is one of the best times to visit, as the snow has fully melted, revealing lush green rice fields and crystal-clear rivers flowing through the village. Some of the centuries-old wooden houses have been transformed into museums, allowing visitors to experience the enduring traditions of the local community. The village also offers charming souvenir shops and authentic regional delicacies to explore.

Tips: Arrive early in the morning to avoid large tour groups that typically arrive later in the day. Be sure to try Hoba Miso, a local specialty where premium local meat and vegetables are grilled on a magnolia leaf with rich miso sauce—an unmissable taste of Shirakawa-go’s culinary heritage.  
 

Hida Takayama

Tucked away in the deep mountain valleys of Gifu Prefecture, Hida Takayama is one of Japan’s underrated cities that transports visitors back in time. This small yet culturally rich town has preserved its Edo-period wooden architecture, creating a charming old-world atmosphere with the majestic Hida Mountains as its backdrop. If you’re drawn to Japan’s history and traditions, Takayama is a destination you shouldn’t miss.

The heart of the town lies in Sanmachi Suji, a beautifully preserved historic district lined with centuries-old wooden buildings, traditional sake breweries, and quaint local shops. Many of these structures date back over 300 years, maintaining the authentic essence of Edo-era Japan.

May is an especially magical time to visit, as Takayama hosts the Sanno Matsuri, one of Japan’s most stunning spring festivals. This celebration features elaborate wooden festival floats parading through the streets, along with rare cultural performances that showcase the region’s deep-rooted traditions.

Tips: Start your morning at Miyagawa Morning Market, a riverside market offering fresh local produce, handmade crafts, and delicious street food. And before you leave, don’t miss the chance to try Hida Beef, a premium-grade Japanese beef known for its incredible marbling and melt-in-your-mouth texture—comparable to Wagyu, but at a more affordable price!  
 

Kegon Falls

For nature lovers exploring Japan’s secondary cities, Kegon Falls is an unmissable destination. Standing at an impressive 97 meters, Kegon Falls is one of Japan’s most breathtaking waterfalls. Located near Lake Chuzenji in Nikko National Park, this natural marvel is at its most spectacular in May. As the mountain snow melts, the waterfall reaches peak flow, surrounded by lush greenery and vibrant wildflowers—making it a perfect spot for sightseeing and photography.

Visitors can enjoy two viewing platforms. The free upper observation deck offers a panoramic view from above, while the lower platform—accessible for a small fee—provides a much closer and more immersive experience. The lower viewpoint is particularly stunning, allowing you to witness the sheer power and beauty of the falls up close. 

Tips: arrive early in the morning for a chance to see a rainbow form over the cascading water. If you plan to take photos from the lower platform, bring a waterproof cover for your camera, as the mist from the falls can be quite strong.

For travelers seeking Japan’s underrated cities rich in nature, culture, and history, Matsue in Shimane Prefecture is a destination you shouldn’t overlook. This charming city perfectly blends scenic beauty with deep-rooted traditions, offering an authentic glimpse into Japan’s heritage.

Known as the “City of Water,” Matsue is nestled between Lake Shinji and Lake Nakaumi, creating a serene and picturesque setting. The peaceful atmosphere makes it an ideal place for a leisurely lakeside stroll, a scenic boat ride, or an immersive experience in the city’s renowned tea culture and traditional tea ceremonies.

If you’re looking to explore Japan’s secondary cities beyond the usual tourist routes, Matsue’s timeless charm and cultural richness promise an unforgettable journey. 
 

Matsue Castle

Matsue Castle is one of only 12 original castles in Japan that have remained intact since the Edo period and is among just five designated as a National Cultural Treasure. Completed in 1611, this historic stronghold sits atop a low hill, surrounded by a picturesque moat and beautifully maintained gardens.

Inside, visitors can explore a collection of ancient weapons, samurai armor, and artifacts from the Edo era. The castle’s top floor offers a breathtaking 360-degree panoramic view of Matsue and its two surrounding lakes. May is an especially scenic time to visit, as the castle gardens come alive with blooming irises and peonies. On select days, visitors can also witness traditional samurai martial arts and archery demonstrations, adding to the immersive historical experience.

Tips: Take a 30-minute boat ride around the castle’s moat, offering stunning views of the fortress from the water. Don’t forget to snap a photo with the centuries-old stone walls, built using a traditional technique without cement—yet still standing strong after hundreds of years.  
 

Lake Shinji

Lake Shinji is Japan’s seventh-largest brackish lake and a defining landmark of Matsue. Not only is it a vital natural resource, but it is also renowned for its breathtaking sunsets. In May, with clear skies and crisp air, the lake becomes the perfect spot to witness the sun’s golden glow reflecting off the tranquil waters—creating a truly mesmerizing view.

Beyond its scenic beauty, Lake Shinji is famous for its Shijimi clams, a delicacy known for its rich flavor and high nutritional value. Early in the morning, you can watch local fishermen heading out in traditional wooden boats to harvest these prized clams—a peaceful and timeless scene bathed in the soft light of dawn.

Tips: For the best sunset views, head to Horikawa Bridge or Yomigaeri Park, both offering stunning vantage points over the lake. And don’t leave without trying Shijimi-jiru, a nourishing miso soup made with fresh Shijimi clams, a local breakfast staple packed with health benefits.  
 

Matsue’s Centuries of Tea Ceremony Culture

Matsue is one of Japan’s most historic cities for green tea culture, deeply rooted in traditional tea ceremonies. It is also known as the home of Lafcadio Hearn (Koizumi Yakumo), a British-Irish writer who fell in love with Japanese culture, including the intricate rituals of the tea ceremony.

For an immersive experience, visit the Meimei-an Tea House, one of Japan’s oldest tea houses and a designated National Cultural Property. Inside, you’ll find a fascinating display of antique tea-making tools and live demonstrations of traditional Japanese tea ceremonies. The surrounding garden is a masterpiece of classic Japanese landscape design, providing a serene and authentic setting to appreciate this centuries-old tradition.

Tips: To complete your tea experience, don’t forget to try Wagashi, a delicate Japanese confection crafted specifically to complement the flavors of green tea.

If you’re looking to explore Japan’s underrated cities, Mie Prefecture is a destination that should be on your list. Nestled along Japan’s Pacific coast, it offers a perfect mix of pristine beaches, sacred shrines, and charming fishing villages, each brimming with history and local culture.

Known for its exceptional seafood and top-quality local ingredients, Mie is a haven for food lovers. May is the perfect time to visit, with warm, pleasant weather that makes exploring the coast even more enjoyable—without the intense summer heat. For those seeking an authentic experience beyond the usual tourist hubs, this secondary city in Japan promises a journey filled with natural beauty, cultural treasures, and unforgettable flavors.  
 

Ise Grand Shrine

More than just a cultural landmark, Ise Grand Shrine is the most sacred site in Shintoism and has long been regarded as Japan’s spiritual heart. Dedicated to Amaterasu, the sun goddess and mythical ancestor of the Japanese imperial family, this revered shrine holds deep historical and religious significance.

Nestled within an ancient cypress forest that has stood for over a thousand years, Ise Grand Shrine exudes a tranquil and mystical atmosphere. Visitors often describe feeling a profound connection to nature and the deep-rooted faith that defines Japan’s spiritual heritage. For those seeking a meaningful cultural experience, this is a destination that should not be missed.

Tips: Before entering the shrine, take a stroll through Okage Yokocho, a charming historical shopping street lined with traditional eateries and souvenir shops. Be sure to try Akafuku Mochi, a beloved Japanese sweet with a history spanning over 300 years.  
 

Toba City: A Coastal Fishing Town

Nestled along the Pacific coast, Toba is a charming fishing town renowned for its fresh seafood, stunning bay views, and world-famous pearls. This hidden gem is home to the Mikimoto Pearl Island, the world’s first successful pearl cultivation site. Visitors can learn about the fascinating history of pearl farming and witness live demonstrations of traditional Ama divers—women free-divers who have been harvesting pearls and seafood for centuries.

May is an excellent time to visit, with warm, pleasant weather making it ideal for a scenic boat tour around Toba Bay. The bay is dotted with over 60 small islands, offering breathtaking coastal landscapes and a glimpse into the region’s thriving oyster farms, seaweed cultivation, and fishing communities.

Tips: For an authentic taste of Toba, don’t miss Ise Ebi (Ise Lobster), a local delicacy known for its sweet, succulent meat. Another unique experience is visiting the AMA Hut Hachiman Kamado, a traditional seaside hut where Ama divers rest and prepare freshly grilled seafood over charcoal, offering a rare insight into their centuries-old way of life.  
 

Iga Ninja Village

For those looking to explore Japan’s underrated cities, Iga in Mie Prefecture is a hidden gem packed with history and adventure. As one of the two most famous ninja origins in Japan, this secondary city offers an immersive journey into the world of ninjutsu, the legendary art of stealth and combat.

At Iga Ninja Village, visitors can explore the Ninja Museum, uncover hidden traps in a traditional ninja house, and watch live demonstrations of real ninja combat techniques. Unlike the portrayals in movies and manga, this experience reveals the true history and skills of Japan’s covert warriors.

For a fun, hands-on experience, visitors of all ages can dress up in ninja attire and capture the moment with memorable photos. Whether you’re a history buff or just looking for something unique, Iga offers a fascinating journey into Japan’s stealthy past.

Looking for the perfect secondary city to explore in Japan? Gunma is an ideal choice! Known for its renowned hot springs, breathtaking nature, and peaceful atmosphere, this Japan underrated city offers a serene escape from the hustle of major tourist hubs.

Despite being just a few hours from Tokyo, Gunma remains relatively undiscovered by international travelers. In May, the weather is ideal for exploring lush landscapes, soaking in natural onsen, and strolling through well-preserved Edo-era villages that capture the essence of old Japan.

If you’re seeking an off-the-beaten-path destination that combines relaxation, tradition, and stunning natural beauty, Gunma is a must-visit.  
 

Kusatsu Onsen

When it comes to Japan’s finest onsen destinations, Kusatsu Onsen consistently ranks among the best. Known for its highly acidic, mineral-rich hot springs, the waters here are believed to have powerful healing properties, particularly for skin conditions and overall well-being.

At the heart of the town lies Yubatake, a massive hot water field that serves as both a primary source of thermal water and a scenic landmark. Every hour, visitors can witness Yumomi, a traditional Edo-era performance where locals stir the hot spring water with wooden paddles to naturally cool it down—all while singing lively folk songs.

In May, the weather is comfortably warm, making it an ideal time to explore the charming streets of Kusatsu or take a leisurely nature walk in the surrounding forests. With fewer tourists than the winter ski season, it’s the perfect moment to enjoy the onsen town at a relaxed pace.

Tips: For an authentic experience, try Jikanyu, a traditional bathing method where visitors soak in an extra-hot onsen for 3-5 minutes at a time. And don’t miss out on Onsen Manju, a local delicacy—steamed red bean buns made using the natural heat of Kusatsu’s hot springs!  
 

Fukiware Falls: The Niagara of the East

Fukiware Falls is often called the “Niagara of the East” due to its impressive 30-meter-wide cascade. Though only 7 meters high, its unique rock formations—shaped by thousands of years of erosion—create a striking landscape of narrow gorges and natural cavities, making it one of Japan’s most fascinating waterfalls.

In May, melting snow from the mountains increases the water volume, creating a dramatic, fast-flowing cascade that’s truly mesmerizing. Surrounding the falls are scenic hiking trails, perfect for nature lovers looking to immerse themselves in the lush greenery of the season.

Tips: Wear sturdy, slip-resistant shoes, as the mist from the falls can make the surrounding area damp and slippery. If time allows, take a stroll along the riverside trail for breathtaking views and a quieter, more secluded experience.  
 

Tsumago Valley

For those who love Japan’s historic charm, Tsumago is a must-visit. Located along the Nakasendo Trail, an ancient route connecting Kyoto and Edo (now Tokyo), this beautifully preserved village feels like a journey back 200 years to the Edo period.

Its cobblestone streets, lined with traditional wooden houses, small shops, and ryokan inns, create an atmosphere untouched by time. To maintain its authenticity, power lines, and vending machines are hidden from view, preserving the village’s old-world appeal.

From Tsumago, travelers can take the scenic 8-kilometer hike to Magome, another picturesque historic village. The walk, which takes 2-3 hours, winds through forests, meadows, and small waterfalls. In May, the trail is particularly stunning, with lush greenery and blooming wildflowers, making it a perfect time for an immersive experience in Japan’s feudal-era landscapes.

Tips: For a hassle-free walk, store your luggage at the tourist information centers in Tsumago or Magome, where it can be sent to the other village. Be sure to try Gohei Mochi, a local specialty—grilled sticky rice skewers coated in a sweet soy sauce glaze—available at village shops.

Exploring Japan’s underrated cities requires a bit more planning than a trip to Tokyo or Osaka, but the rewards are worth it! You’ll experience breathtaking natural landscapes, rich cultural heritage, and a peaceful atmosphere away from the usual crowds. Here’s how to navigate secondary cities efficiently while making the most of your budget.  
 

JR Pass – A Cost-Effective Option for Multi-Region Travel

If you’re visiting multiple prefectures, the Japan Rail Pass (JR Pass) is a great way to save on train fares. However, not all secondary cities are directly accessible via JR lines, so check if additional local trains are needed for your destination.

Tips: Consider JR Regional Passes, such as the Kansai Wide Area Pass or Hokuriku Arch Pass, which cover specific areas and may be more cost-effective than a nationwide JR Pass.
 

Local Trains – The Best Way to Explore Within Prefectures

Many prefectures offer discounted travel passes for tourists, covering local train routes and helping cut transportation costs. Some excellent options include:
 

• ● Gunma Free Pass – deal for exploring Gunma’s onsen towns and natural attractions.
• ● Mie Kintetsu Rail Pass – Perfect for visiting Ise Grand Shrine and Iga Ninja Village.

Buses – Reaching Destinations Beyond the Rail Network

For places where trains don’t reach—such as Shirakawa-go or remote mountain villages—buses are the most reliable option.

Popular bus routes include:
 

• ● Nohi Bus – Connects Takayama and Shirakawa-go, a must-visit Japan underrated city.
• ● Willer Express – A highway bus service linking major cities with secondary cities.

Car Rentals – Ultimate Flexibility for Rural Exploration

For travelers seeking independence and convenience, renting a car is the best option—especially in rural areas where public transportation is limited. A self-drive trip allows you to visit hidden gems in Japan’s secondary cities at your own pace.

Want to know more about renting a car in Japan? Click here for a complete guide!

If you’re planning a trip to Japan, why not step off the beaten path and explore Japan’s secondary cities? These hidden gems offer peaceful atmospheres, breathtaking natural landscapes, and authentic local culture—all while supporting local communities and uncovering unique stories you won’t find in the usual tourist hotspots.

With Gother, exploring four must-visit secondary cities is easier than ever. Book flights, accommodations, activities, and car rentals all in one place—plus, enjoy exclusive deals for a trip that’s both seamless and unforgettable. Reserve your adventure today and see Japan from a whole new perspective!