Japan is a fascinating country that offers a unique experience to all its visitors, whether they’re looking to explore a big city or see places off the beaten path. We’ve already made a Japan day-by-day itinerary that covers all the major cities in Japan, so this guide will focus only on the hidden gems that aren’t swarming with tourists.
An island with more cats than people, a stunning national park, and the prettiest lake in the country are just a few of the beautiful places in this guide. Read on to see all the wonderful hidden gems in Japan, so you can prepare for an upcoming trip!
Geibikei Gorge is one of Japan’s best-hidden gems in the Iwate Prefecture. This ravine on the Satetsu River has been declared a National Place of Scenic Beauty, which is just one of many reasons why it’s worth visiting even if it’s not on every list of best places to visit in Japan.
Boat rides through the gorge are very popular here, especially among visitors who want to admire the scenic nature of Japan off the beaten path. The area surrounding Geibikei Gorge is full of hiking trails, scenic spots, waterfalls, and other beautiful sights worth exploring.
Kamikochi is a vast national park in the Hida Mountain range in central Japan. It is very popular with both foreigners and locals who want to explore Japan and its many hidden gems, thanks to the abundance of interesting sights and things to do in the surrounding area.
Kamikochi features a river, a scenic valley, mountains, hot springs, and too many hiking trails to count. The national park is one of the most popular tourist destinations in the Japanese Alps, but it still remains one of the best-hidden gems in this amazing country.
Lake Biwa is a pretty big freshwater lake northeast of Kyoto. You can easily visit it on a day trip from this popular city, making it one of the hidden gems in Japan that are the easiest to find.
The beautiful lake is known for its spectacular nature, large fish population, and excellent birdwatching opportunities. Also, there are quite a few resorts and beaches on its shoreline, so it’s a great place for a relaxing vacation in Japan.
In addition to mesmerizing nature and beachside resorts, Lake Biwa is also known for the many surrounding historic sites. It’s home to the Hikone Castle, the Enryaku-ji Buddhist temple complex, and the Lake Biwa Museum.
This Japanese museum is a great place to visit if you want to learn more about the natural and cultural history of the region.
Ine is a small seaside village north of Kyoto Prefecture. The quaint fishing village is best known for the wooden boathouses that line its docks and beaches. The boathouses are collectively known as funaya, and they’re one of the top tourist spots in this charming village.
The funaya are popular for their atypical architecture – their first floors are reserved for storage of boats and fishing gear, while the upper floors usually feature living quarters.
Ine boathouses have been designated a Group of Historic Buildings, and most of them aren’t available for rent. There are a few waterfront inns tourists can stay at, but the best way to really experience these wooden boathouses is to book a boat tour and see them from the sea.
Fukui is the capital city of the Fukui Prefecture, and it’s one of a few cities that can be considered a hidden gem of Japan. With a total population of some quarter of a million, Fukui is a pretty small city when it’s compared against the famous urban metropolises of Japan like Tokyo and Kyoto.
Fukui doesn’t get nearly as many tourists as other Japanese cities, so it’s a great place for all travelers who want to explore Japan’s more urban areas but are terrified of the crowds.
Although it’s not exactly one of the hottest tourist spots, there are enough things to see and do in Fukui that you can easily find things to keep you occupied for days. Castle ruins, a sprawling park full of cherry blossoms and monkeys, gardens, museums, and many beautiful shrines can all be found throughout Fukui.
It’s also worth noting that the city is close to the northern coast, which features beaches, even more shrines, and quite a few other hidden gems worth checking out.
Matsuyama is the capital city of Ehime Prefecture. It is situated on Shikoku island, which is one of Japan’s three main islands that surround the Seto Inland Sea.
Matsuyama is an old city, which is best known for its many hot springs. The onsens are very popular with visitors, but they’re certainly not the only reason why this Japanese city should be on your radar.
Matsuyama has several tourist attractions that are several centuries old, so it’s the perfect place if you want to explore more of Japanese history. With onsens from the Meiji Period, a medieval castle, and stunning Buddhist temples, Matsuyama doesn’t disappoint when it comes to interesting sights.
Nagano is one of the most important cities in hidden Japan. It’s one of the oldest cities in the country, as well as the capital of the Nagano Prefecture, and yet it barely gets a fraction of the tourists that Tokyo, Kyoto, and Kobe do.
Nagano is known for many things – onsens, world-class ski resorts, Buddhist temples, winter Olympics, and a lot more. The charming city is home to Jigokudani Monkey Park, which is world-famous for its snow monkeys that enjoy soaking in their own onsen.
In addition to ancient temples, snow monkeys, and exhilarating ski pistes, Nagano is also known for medieval ruins, too many cherry blossoms, and spectacular mountain views.
If you’re visiting Japan and want to explore a big and important city but preferably without huge tourist crowds, Nagano is certainly one of the best-hidden gems in Japan to consider.
The Izu Peninsula is a large peninsula south of Mount Fuji and west of Tokyo, on Japan’s main island of Honshu. It is easily accessible from Tokyo by roads and railways, so it should be easy to reach it during your Japan trip.
The peninsula is known for beautiful beaches, nature parks, gold mines, and excellent resorts. It’s a pretty popular vacation spot in Japan, but it’s not as busy as the cities that are most popular with tourists.
Check out this hidden gem in Japan if you want to visit onsens, see black sand beaches, explore mountainous hiking trails, and indulge in sea bathing, surfing, and even golfing.
Otaru is a port city in Hokkaido, the northernmost island in Japan. The city had a key role in the fishing industry of Japan, and there are many museums and buildings throughout the town that are a testament to its importance.
There’s a former fish processing plant that was built in Otaru in 1897, and it’s one of the most popular attractions in the city. Other popular spots in the port town include sake distilleries, music boxes, and the town’s many museums.
Additionally, it’s worth noting that Otaru is a Japanese city with a rich glass working history, with several shops that are more than a century old. If you’re looking for places off the beaten path that are worth exploring in northern Japan, Otaru is certainly one of the best options.
Yakushima Island is a small island in southern Japan. Situated off the southern coast of Kyushu Island, Yakushima Island is a UNESCO World Heritage Site that without a doubt deserves the title of a Japan hidden gem worth visiting. Yakushima is famous for lush forests, a gorgeous coastline, and beautiful views that are simply out of this world.
This stunning island is home to the largest nesting ground of the loggerhead sea turtle, and it’s home to a unique remnant of the temperate ancient forest. The latter is actually the reason why the island has gained the status of a world heritage site, and another great reason to visit this amazing hidden gem.
Nasu is a small town in the Kantō region of Japan. It’s situated northeast of Tokyo, at the foot of Mount Nasu, which is a group of volcanoes. The volcanoes are part of the Nikkō National Park, and one of the key reasons why this hidden Japanese gem is attracting more and more tourists!
In addition to spectacular volcano views, Nasu also boasts lakes, parks, valleys, and unique museums. Whether you’re looking to spend your time in Japan exploring different hiking trails, or you want to visit a museum that’s all about classic cars, Nasu is a hidden gem that will certainly not disappoint.
Sado Island is a hidden gem in Niigata Prefecture, best known as being the place where political opponents were exiled up to the 18th century. Although the island’s history is a bit dark, that doesn’t stop it from being one of the more popular attractions in this part of Japan.
Sado Island is popular for its stunning beaches, rice terraces, gold mines, and scenic driving routes. The island promises panoramic views for days, and you can even try your hand at gold panning and go on tub boat rides. There are lots of fun things to see and do on Sado Island, which makes it one of the top hidden gems that are worth visiting in Japan!
Tashirojima is an island in the Miyagi Prefecture, with just some 80 permanent residents. What makes this tiny island special is the huge population of stray cats, which earned it the nickname “cat island”.
Japan’s cat island is the absolute perfect hidden gem for all tourists who visit Japan and can’t get enough of the cat cafes throughout the country. It’s believed that cats bring luck and good fortune to people, so the locals of the island fed them, which led to Tashirohima ultimately having a larger feline than the human population.
Matsuzaki is a town on Japan’s Izu Peninsula, and one of the best places to visit if you want to further explore the gorgeous peninsula and all its attractions. The small town is known for scenic views of its many rice terraces and beaches, but that’s certainly not the only reason to explore Matsuzaki.
Travel to this gem off the beaten path to spend some time in one of Japan’s warmer regions, while exploring the numerous hiking trails and onsens that Matsuzaki is known for in Japan.
Also, it’s worth noting that Matsuzaki is in a hilly region, which means there are quite a few fun and exciting walking trails to explore just outside the main town area.
Okunoshima is a very small island southeast of Hiroshima. It’s locally known as Japan’s Rabbit Island, mostly because there are so many wild rabbits roaming around the island.
The good news is that the rabbits are tame and they often approach humans. They are absolutely adorable, and you can even feed them, pet them, and play with them if you want.
Traveling to a remote island in the Seto Inland Sea just to play with wild rabbits might sound a bit crazy, but it’s certainly a fun thing to do while exploring Japan off the beaten track!
Kyushu Island is one of the three main Japanese islands, so it’s not exactly a secret spot. However, it’s safe to call it one of Japan’s hidden gems since not many people who have visited Japan have actually made it to Kyushu island.
It’s closer to South Korea than to Tokyo and Kyoto, it’s not home to that many famous tourist attractions, and it’s not exactly known for thrilling architecture.
However, Kyushu Island is the ideal place in Japan for all nature lovers. It’s known for its breathtaking scenery, lush forests, and gorgeous views no matter where you look.
If you want to hike volcanoes, see beautiful villages, and bathe in a hot spring or two, consider traveling to Kyushu on your first visit, instead of just adding it to your next Japan itinerary.
Nishio is a city in Aichi Prefecture in southern Japan. It is south of Nagoya, and it’s the perfect place to explore on a day trip if you’re staying in one of Japan’s busier tourist hubs.
The city is best known for the Nishio Castle, which was originally constructed in 1221 during the Kamakura period. Although many of the top attractions in Nishio City are quite old and a testament to its rich history, Nishio is not just about Japanese folklore and traditions.
The city is a great place to explore the glassblowing culture of Japan, plus it’s home to quite a few intriguing technology museums. Nishio also boasts many onsens, delicious street food, as well as some stunning beaches that are too easy to enjoy.
Anna is the co-owner of expert world travel and can't wait to share her travel experience with the world. With over 54 countries under her belt she has a lot to write about! Including those insane encounters with black bears in Canada.