10 Little-Known Towns and Villages Worth Visiting in Japan
I know, when you hear Japan, you instantly think of Tokyo. But, here’s the deal.
If you want to feel the real magic of Japan, forget Tokyo and visit towns and villages that are not so crowded. Instead they offer you the true Japanese tradition that lives for ages!
If you’re looking for a travel experience that’s authentic, unforgettable, and full of wonder, these hidden destinations in Japan will capture your heart and leave you longing for more.
Get ready to explore a side of Japan that few ever see.
1. Shirakawa-go (Gifu Prefecture)
Hidden in the Japanese Alps, Shirakawa-go looks like something straight out of a fairy tale… especially in winter when it’s steep, farmhouses sit under a thick blanket of snow.
These gassho-zukuri homes, named for their “praying hands” shape, were designed to withstand heavy snowfall, and some are over 250 years old! Walking here is like going back into another dimension!
You can wander inside some of the farmhouses, like the Wada House, to see how families lived for generations. Another great choice is to try gohei mochi, a grilled rice cake slathered in sweet miso.
Hurry up with the booking! Everyone wants to experience this magic!
2. Ine (Kyoto Prefecture)
Imagine waking up to the sound of waves lapping beneath your feet. Literally! In Ine, a fishing village on the coast of Kyoto Prefecture, houses called funaya are built right over the water. And they blend beautifully with the sea.
Fishermen once used the first floors of these boat houses to dock their vessels, while the upper floors served as cozy living spaces. Today, some of these 200-year-old houses have been converted into charming inns.
So, grab the opportunity to sleep above the ocean!
3. Tottori (Tottori Prefecture)
Japan may not have vast deserts, but Tottori comes close.
The Tottori Sand Dunes stretch over 30 square kilometers. This is still Japan, not the Sahara, if you feel confused!
Here, you can ride camels, try sandboarding, or simply roll down the dunes like a carefree kid, no judgments from me. And the best part? Climbing to the top rewards you with a stunning contrast of golden sand meeting the deep blue of the Sea of Japan.
Food lovers, get ready! Tottori is famous for its matsuba crab, considered one of the best in Japan. It’s only available in winter, but trust me, it’s worth the trip. Imagine buttery, melt-in-your-mouth crab legs straight from the source. Pure seafood heaven!
4. Ouchi-juku (Fukushima Prefecture)
If you’ve ever dreamed of wandering through an Edo-period town, Ouchi-juku is your chance. This former post town once bustled with travelers making their way to Edo (modern-day Tokyo).
Today, its dirt roads and houses look almost exactly as they did centuries ago, transporting you to an era of samurai, merchants, and hidden mountain villages.
For a perfect view, hike up to the Ouchi-juku viewpoint, where the rooftops form a beautiful line against the mountain backdrop. If it’s possible, visit in winter. This is when the whole town turns into a snowy wonderland. A real-life samurai film!keeping the historical vibe intact. It’s a perfect spot for history buffs and romantics alike!
5. Taketa (Oita Prefecture)
Taketa is a small town with a big history.
Once a thriving castle town, it’s now home to the Oka Castle Ruins, an beautiful site where moss-covered stone walls stand as a quiet reminder of Japan’s feudal past.
It’s so atmospheric that it inspired the famous song Kōjō no Tsuki (The Moon Over the Ruined Castle), which is still sung across Japan today.
If relaxation is your thing, the town is also known for its carbonated hot springs, said to be among the best in Japan. Soak in the bubbling waters, and you’ll emerge feeling brand new.
And since it’s just a short trip from Beppu’s famous hot springs, why not make it a double adventure?
6. Yakushima (Kagoshima Prefecture)
Step into Yakushima, and you’ll feel like you’ve entered a forest straight out of a Ghibli movie, because, well, you have.
This island, covered in ancient cedar trees, was the real-life inspiration for Princess Mononoke. The most famous tree here, Jōmon Sugi, is estimated to be over 7,000 years old, making it one of the oldest living things on Earth.
The trails range from gentle strolls to full-on 12-hour treks, but every step is worth it. Along the way, you might spot adorable Yakushima macaques or the tiny native deer, both of which roam freely across the island.
And let’s talk about the rain! Yakushima is famous for its near-constant drizzle, but that’s what gives the island its magical atmosphere.
7. Gujo Hachiman (Gifu Prefecture)
This little town is tucked away in the mountains of Gifu, and it’s known as the “Water City” because of its crystal-clear canals and rivers that run through the streets. Seriously, it feels like something out of a movie.
It’s so clean that locals still use the waterways to wash vegetables and even chill their drinks!
You can wander through narrow streets lined with old wooden houses, cross little stone bridges, and stop by the local shops selling everything from traditional sweets to hand-crafted souvenirs.
And the view from Gujo Hachiman Castle? Unreal.
8. Nagatoro (Saitama Prefecture)
If we’re up for a little adventure and nature escape, you’ve gotta hit up Nagatoro. It’s just a short train ride from Tokyo, but it feels like a world away.
It’s a fantastic spot for hiking, especially in autumn when the hills explode into strong reds and oranges.
The area is home to the Hodosan Shrine, a peaceful sanctuary surrounded by forests, and if you’re up for a view, the Hodosan Ropeway will take you to the top for a panoramic look at the Chichibu region.
9. Shodoshima (Kagawa prefecture)
Shodoshima, or “Small Bean Island,” is Japan’s answer to the Mediterranean, famous for its olive groves, sandy beaches, and coastal cliffs.
The island has been cultivating olives for over a century, and you’ll find olive-themed everything, from gelato to skincare products.
There’s even an Olive Park, complete with Greek-style windmills, where visitors love reenacting scenes from Studio Ghibli’s Kiki’s Delivery Service by posing with broomsticks. Hilarious!
10. Kamikatsu (Tokushima Prefecture)
Kamikatsu is charming, yes! But, more than that it’s a recycling utopia. This tiny town in the mountains of Tokushima Prefecture has set out to become Japan’s first zero-waste town, sorting garbage into over 45 different categories.
But don’t worry, this isn’t a story about trash! It’s about sustainability, creativity, and a community making eco-friendly living look incredibly stylish.
Beyond its sustainability efforts, Kamikatsu is a hiker’s dream. The Mount Yamainudake trail offers incredible views of green mountains and misty valleys. Whenever I think of natural beauty, my mind goes here. And once you visit it, I’m sure, yours will too!