Magical places you must visit in Japan that aren’t Tokyo or Kyoto

While Tokyo and Kyoto reign as Japan’s most popular destinations, the country offers so many other magical places worth exploring beyond the usual suspects. From beautifully remote islands and seaside towns to mountain villages enveloped in nature, Japan has a wealth of unique locales waiting to be discovered.

1. Cape Shiretoko (Hokkaido)

[Cape Shiretoko in Hokkaido, Japan][

Perched on Japan’s northernmost island of Hokkaido, Cape Shiretoko is one of the country’s most visually stunning natural destinations. Designated a UNESCO World Heritage site, the rugged peninsula is blessed with pristine beaches, dense forests, and crystal clear waters teeming with marine life.

In spring, you can spot brown bears foraging in river valleys, while summertime brings dancing fireflies illuminating coastal woodlands at night. Autumn paints the landscape shades of red and gold before winter cloaks the cape in a blanket of snow. For pure natural splendor, it’s hard to rival Cape Shiretoko.

The easiest way to access this remote region is by car, allowing you to stop wherever the unfolding scenic panoramas please you most. Hike coastal trails for breathtaking ocean vistas or spot whales and puffins from ocean viewing platforms. For accommodations, consider family-run ryokans in the small fishing village of Shari that can arrange guided tours.

Local guide Hiro Tanaka shared: “Cape Shiretoko is truly magical—a place where you feel connected to nature’s beauty and rhythms. It has a special energy and is worth braving the drive to escape crowded tourist spots.” Plan at least 2-3 days to soak up the Cape Shiretoko magic.

2. Naoshima (Seto Inland Sea) [Yellow Pumpkin sculpture at Benesse Art Site Naoshima][

Nestled in Japan’s Seto Inland Sea is the island of Naoshima, which has transformed into an outdoor art museum dotted with installations by top artists like Andy Warhol and Claude Monet. Spending a day wandering Naoshima is like immersing in a surreal dreamscape, with art integrated seamlessly into the coastline’s natural splendor.

Some highlights include Yayoi Kusama’s pumpkins lit up at night, James Turrell’s sky-gazing mound, and a 3D Monet water lily mural. There are also art houses in the woods and galleries showcasing works from Japanese masters. The nearby islands of Teshima and Inujima hold additional cutting-edge installations.

Naoshima embraces art as a way to elevate one’s perspective and connect to beauty. Rather than feeling like a typical “tourist attraction,” the integrated works invite reflection on nature, perception, and humanity’s place. The unspoiled coast and hospitality also imbue the experience with a meditative quality.

For lodging, consider the Benesse House, a Pritzker Prize-winning hotel with art-filled rooms facing the sea. Make time to relax in an onsen, go cycling around the island, or dine at the harbor-front restaurants serving local seafood. Allow 2-3 days to fully absorb Naoshima’s magical art-meets-nature vibe.

3. Hiraizumi (Tōhoku Region) [Chuson-ji Temple complex in Hiraizumi, Iwate Prefecture]

Nestled in northern Japan’s lush green Iwate Prefecture is the historic town of Hiraizumi. Once the capital of the 12th-century Fujiwara clan, it’s home to three exquisite World Heritage sites that conjure up images of Japan’s golden imperial past.

Top billing goes to the Chuson-ji Temple complex, with its ornate wooden buildings, stone carvings, and stunning lotus-filled pond representing paradise. Nearby, the Mōtsū-ji Temple features the distinctive “Pure Land” architectural style with golden images of Buddha. Both hide magical gardens perfect for a meditative stroll.

For a sense of how the nobility lived, visit the ruins of Konjiki-dō, a sumptuous gold-plated structure filled with beautiful sculptures. The rebuilt Tamagawa Onsens then offers a chance to soak tired muscles in hot springs and reflect on simpler times.

Local guide Keiko Sato shared: “There’s a real mystical atmosphere walking these ancient temple grounds, like stepping back in time. Experiencing Hiraizumi’s meticulously preserved heritage gives insight into Japan’s cultural depth.”

Plan to explore the sites over 2 days, staying in a ryokan near the old capital. From spring to autumn different events also bring the heritage alive through dances, craft demonstrations and tea ceremonies.

4. Inland Sea Islands [Torii gate and forest on Inujima Island]

Japan’s scenic Inland Sea is dotted with over 3,000 islands ripe for exploration. Aside from Naoshima, other lesser-known gems hold their own doses of natural and cultural magic:

Shodoshima: Known as “olive island,” Shodoshima abounds with orchards and wineries. Rent a bike to leisurely ride paths amid rolling hills and farmscapes.

Ikuchi Island: An unspoiled isle famous for pristine beaches and “angel roads” nestled between pine forests and ocean views.

Inujima: Transformed by artist interventions like a “seafloor art museum” visible from trails. Take copper mine tours and stay at a hilltop ryokan.

Ogijima: Visit a historic post town filled with Meiji-era buildings and quaint shops selling local crafts like baskets and ceramics.

The islands are easily accessed from major cities like Okayama via local ferries. A car isn’t needed to leisurely explore the laidback villages, coastlines, and rich sea harvests like scallops and oysters, all surrounded by azure waters. Consider island-hopping over a week to fully unwind in the Inland Sea’s restorative natural settings.

5. Tsumago and Magome (Kiso Valley) [Old post town of Magome along the old Nakasendō trail]

Nestled deep in the Japanese Alps lies the enchanting Kiso valley – home to the well-preserved post towns of Tsumago and Magome along the former Nakasendō trade route. Wander winding cobblestone paths connecting historic inns, shrines, and tea houses that have stood for centuries.

Magical details around every corner transport you back in time, from samurai guardhouses and rice-straw-covered bridges to clear mountain streams. Stay overnight at a ryokan in a tatted futon for an authentic cultural experience. In Tsumago, don’t miss eating smoked salmon served in bamboo sheaths at a local restaurant.

After exploring on foot, continue the magical journey by taking the Kiso Railway, one of the few remaining mountain lines pulled by steam locomotives. Wind through dense forests and rice terraces for breathtaking views of rural Japan is rarely seen from highways.

The idyllic Kiso Valley instills a real sense of stepping back in time. Local guide Mariko Ono commented: “Walking these moss-lined paths in Magome and Tsumago, I feel like I’m discovering buried treasures around every corner. It’s a place to truly unwind from modern life.” Plan an overnight or two to fully soak up the magical atmosphere.

6. Shimokita Peninsula (Aomori) [Coastline of the Shimokita Peninsula in Aomori Prefecture]

On Japan’s northern coast lies the remote Shimokita Peninsula in Aomori – an unspoiled natural paradise waiting to be explored. Rugged coastlines of steep cliffs and rocky formations alternate with sheltered coves and beaches teeming with sea life. In spring, fields bloom in shades of yellow and purple blossoms, overlooking the rolling surf.

Activities include hiking rugged capes and taking photographs of coastal rock formations shaped by wind and waves. For a memorable experience, join a guided boat tour through craggy islets and sea caves to spot dolphins, eagles, and, if lucky, whales.

To fully unwind, visit one of the peninsula’s hidden onsen towns like Osado, located along picturesque rivers flowing into the sea. Stay at a traditional ryokan and have a meal with local seafood specialists serving everything from scallops to squid harvested that day.

It’s hard to find a place more dramatically scenic than Shimokita’s wild coastlines. With patient observation, secrets of nature reveal themselves through the grandeur of this hidden realm. Two to three nights here allow for restorative downtime in one of Japan’s last unspoiled spaces.

7. Takachihō (Central Japan Alps)

[Takachihō shrine complex nestled in the mountains]

In Nagano’s Chino region sits the magnificently isolated Takachihō shrine atop a mountain peak. Making the arduous hike or ropeway ride up awards visitors with a magical experience that is hard to find elsewhere.

Takachihō is believed to be one of Shugendō’s most sacred sites – a historical blend of Buddhism, Shinto, and mountain worship. Venture along winding paths through ancient cedar and cypress groves interspersed with moss-laden rocks. Pause to admire delicate carvings and paintings adorning centuries-old structures.

At the summit lies a quiet shrine complex more like a mystical world unto itself. Bathe in icy mountain waters is said to cleanse both body and soul. Takachihō’s rites aim to purify one’s spirit through communing with nature – an experience that leaves a deep impression long after leaving.

Allow a full day to slowly explore the shrine’s magic. Opt to overnight at a nearby ryokan like Nunoya to further unwind in the soothing nature. Takachihō’s tranquility offers an antidote to modern stress amid Japan’s deep spiritual heritage.