There are hundreds hot springs (onsen) across Japan. Below is a list of some of the best of them.

Kansai (West part of Japan around Kyoto and Osaka)

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Kinosaki Onsen
Kinosaki Onsen is a charmingly old-fashioned onsen town near the Sea of Japan coast. In the evenings guests of the local ryokan stroll about town in yukata and geta, visiting public baths and nostalgic game arcades.
Arima Onsen
Located still within the city limits of Kobe and just an hour outside of central Osaka, Arima Onsen is one of the Kansai Region’s most popular hot spring resorts. It is also one of its oldest.
Katsuura Onsen
Katsuura Onsen is a coastal hot spring resort on the Kii Peninsula. It is smaller than nearby Shirahama, but still boasts several huge hotel complexes. Katsuura is located not far from Nachi Taisha, one of the three Kumano shrines.
Shirahama Onsen
Shirahama Onsen is ranked both as one of Japan’s three largest and oldest hot spring resorts. It comes with a white sand beach, coastal rock formations and several amusement parks, and is a popular playground for the urban population of Greater Osaka.

Hokkaido

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Noboribestu Onsen
Noboribetsu is the most famous hot spring resort in Hokkaido, and its spectacular Jigokudani (“Hell Valley”) is the source of some of the country’s highest quality hot spring water.
Kamuiwakkayu Falls
Kamuiwakka is a warm mountain stream in the unspoiled Shiretoko National Park. Bathers need to climb up the stream for about 20 minutes until reaching a natural basin below a hot waterfall, however, due to the danger of falling rocks, the upper, most attractive part has been closed in recent years.
Toyako Onsen
Toyako Onsen is a hot spring resort located at the shores of beautiful Lake Toya and at the foot of Mount Uzu, a volcano which most recently erupted in the year 2000.
 

Kanto(East part of Japan around Tokyo)

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Kusatsu Onsen
For centuries, the abundant hot spring waters of Kusatsu Onsen have been considered among Japan’s best and most effective, if not the best. Much of the resort’s water bubbles up in the yubatake (“hot water field”) in the town center.
Manza Onsen
Located at an altitute of 1800 meters above sea level, this hot spring resort offers by far the most sulfuric waters in Japan. In winter, it is a great destination for enjoy an open-air bath in the snow.
Hakone Onsen
Easily reached from Tokyo and one of Japan’s most popular hot spring resorts, Hakone boasts a large number of hot springs in beautiful setting along the forested valley and the shores of Lake Ashinoko.
Minakami Onsen
Over a dozen hot springs are spread over the large rural area covered by Minakami Onsen at the foot of Mount Tanigawa. Among the resort’s most popular baths are the large riverside rotemburo of Takaragawa Onsen and the traditonal, wooden indoor baths of secluded Hoshi Onsen.
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Nasu Onsen
Nasu Onsen is a hot spring resort in the highlands below Mount Nasudake. The atmopsheric Shika no Yu indoor bath with multiple wooden tubs of varying temperatures is outstanding.
Nikko Yumoto Onsen
Several hot springs are located at the foot of Mount Nantai, a sacred, extinct volcano in Nikko National Park. Among them are Chuzenji Onsen at the shores of Lake Chuzenji and Yumoto Onsen.
Ikaho Onsen
Located on the slopes of Mount Haruna, Ikaho Onsen is well known for its stone stairs leading through the town center and its iron rich thermal waters.
Kinugawa Onsen
Located within easy reach of Tokyo, Kinugawa Onsen has grown into one of Japan’s most developed hot spring resorts. The beautiful Kinugawa River is lined by huge ryokan buildings, while several interesting theme parks provide more entertainment nearby.
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Shiobara Onsen
Shiobara Onsen is a quite built up hot spring town, but thanks to its location in a steep, forested valley, it feels quite pleasant. The town offers multiple good baths, some nice waterfalls and multiple pedestrian suspension bridges.
Shima Onsen
Shima Onsen is an onsen town, stretching along a forested valley in the mountains of northern Gunma Prefecture. It feels calmer and less developed than many other hot spring towns.
  

Kyushu

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Kurokawa Onsen
Kurokawa Onsen is one of Japan’s best hot spring resorts, both in terms of its pretty, traditional town center and its outstanding outdoor baths.
Beppu Onsen
Beppu is Japan’s onsen capital. No other resort produces more hot spring water and few resorts can compete with the city’s large array of hot spring baths. Among Beppu’s attraction are various hells, hot springs not suited for bathing.
Yufuin Onsen
Not far from Beppu, Yufuin is a rural hot spring town, which offers a unique atmosphere somewhat different from a regular hot spring resort. Besides its baths, Yufuin attracts with its cafes, boutiques and art galleries.
Kirishima Onsen
Kirishima Onsen is a collection of several hot spring resort at the base of the Kirishima Mountains in Kirishima National Park.
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Unzen Onsen
Unzen Onsen is a pleasant hot spring town on the slopes of Mount Unzen, offering strong, sulfuric waters that surface in hot spring fields around the town.
Ibusuki Onsen
The seaside town of Ibusuki on the Satsuma Peninsula near the southern tip of Kyushu is famous for its sand baths.
  

Chubu

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Okuhida Onsen
The Okuhida region in a valley deep in the Northern Japan Alps offers five hot spring towns with some of Japan’s most spectacular outdoor baths. Many of the baths come with views of surrounding peaks of the Northern Alps.
Shibu Onsen
Shibu Onsen is a small, old-fashioned onsen town with wooden ryokan and nine small public bath houses scattered around town. Not far from Shibu Onsen, monkeys enjoy hot spring bathing, at the Jigokudani Monkey Park.
Shirahone Onsen
Shirahone Onsen is a loose collection of a dozen or so ryokan in a steep valley in the Northern Japan Alps. The town is known for its milky hot spring water.
Gero Onsen
One train hour south of Takayama and 90 minutes north of Nagoya, Gero Onsen is one of Japan’s most famous hot spring resorts.
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Kaga Onsen
Kaga Onsen is a collection of four historic hot springs towns south of Kanazawa: Yamashiro Onsen, Yamanaka Onsen, Katayamazu Onsen and Awazu Onsen.
Wakura Onsen
Wakura Onsen is a hot spring resort located beside Nanao Bay on the Noto Peninsula. The resort town is dominated by massive ryokan complexes, the most famous of which is the Kagaya, which consistently ranks among Japan’s best ryokan for its excellent service and facilities.
Togura Kamiyamada Onsen
What differentiates Togura Kamiyamada Onsen from your average onsen town is the presence of Tyler Lynch, a tall American who runs one of the local ryokan and contributes to making the town very accessible to foreign tourists. Togura Kamiyamada is, furthermore, home to a reconstructed mountain fortress from the era of warring states.
 

Shikoku

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Dogo Onsen
Dogo Onsen is considered one of Japan’s oldest hot spring resorts, and it is said that Prince Shotoku has already enjoyed the area’s hot spring waters about 1500 years ago.