Best Boutique Hotels in Japan

List Of Best Boutique Hotels Japan

We have created a list with the best boutique hotels in Japan. Hope you enjoy it. We think it might be the best of its kind around

boutique hotels in Japan
Hotel
414-0055 Shizuoka, Ito, Oka 203 , Japan

Seizan Yamato is nestled on a beautiful hill with stunning views of Ito City and the calm blue ocean. This serene location combines the beauty of nature with the warmth of modern Japanese design, creating a welcoming atmosphere. We invite you to relax and feel at home while enjoying delicious, freshly prepared meals that celebrate local flavors.

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Boutique hotel amenities:

Child Friendly • Hot Tub

boutique hotels in Japan
Hotel
600-8113 Kyoto, Kyoto, Hashidono-cho 362-3, Shimogyo-ku, Japan

Genji Kyoto is a welcoming hotel that offers a variety of amenities to make your stay comfortable and enjoyable. You can explore the beautiful city of Kyoto by borrowing one of our free bikes, or simply relax in our lovely garden. We also have a shared lounge and a terrace where you can unwind and connect with others. For your dining needs, we have an on-site restaurant and room service available to ensure you have delicious meals whenever you want. Our friendly staff is here to help 24 hours a day, so you can feel at ease knowing assistance is always within reach. We look forward to making your visit to Kyoto a memorable one!

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Boutique hotel amenities:

Entertainment • Child Friendly • Sports/Activities • Restaurant

boutique hotels in Japan
Hotel
389-2253 Nagano, Iiyama, Iiyama 11492-331, Japan

Welcome to Snowball Chalet at Madarao Mountain! Nestled in the beautiful Japanese Alps, our chalet is just a quick 100-minute train ride from Tokyo, making it an easy getaway for everyone. We understand how important connectivity is, so we offer free WiFi throughout the chalet to help you stay connected with friends and family during your stay. Whether you're here to relax or explore the stunning scenery, we’re committed to making your experience comfortable and enjoyable. We can’t wait to welcome you!

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Boutique hotel amenities:

Wellness Facilities • Transportation/Shuttle • Entertainment • Restaurant • Hot Tub • Sports/Activities • Skiing • Child Friendly

boutique hotels in Japan
Hotel
602-8252 Kyoto, Kyoto, Kamigyo-ku Kamichojamachi Kitakodaimoncho 548-1, Japan

Mugen is a beautiful property that has stood for 160 years in the heart of Kyoto, just a short 1 km walk from the historic Nijo Castle. Each room at Mugen is designed with your comfort in mind, offering a private shower room and toilet, along with complimentary toiletries and a hairdryer for your convenience. We also provide free WiFi to help you stay connected during your stay. Whether you're here to explore the culture or relax, we aim to create a welcoming space for everyone.

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Boutique hotel amenities:

Entertainment

boutique hotels in Japan
Hotel
949-2223 Niigata, Myoko, Tarumoto 1101-215, Japan

Nestled in the beautiful area of Myoko, Onpoint Madarao offers a warm and welcoming place to stay just 25 km from Ryuoo Ski Park. Our accommodations include comfortable rooms and access to a lovely garden where you can relax and unwind. We provide free private parking for your convenience, as well as a shared lounge where you can connect with others. Enjoy delicious meals at our on-site restaurant, making your stay even more enjoyable. If you're looking to explore, we're also located 31 km from Jigokudani Monkey Park and 33 km from other local attractions. We look forward to making your visit memorable!

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Boutique hotel amenities:

Child Friendly • Skiing • Entertainment • Restaurant • Sports/Activities

boutique hotels in Japan
Hotel
044-0081 Hokkaido, Kutchan, Yamada 170-248, Japan

Welcome to Kimamaya Boutique Hotel, your cozy retreat in the heart of Hirafu Village. Just a quick 10-minute taxi ride from JR Kutchan Station, we’re conveniently located and ready to welcome you. Here, you'll find comfortable and stylish rooms designed for relaxation after a day of exploring. Enjoy complimentary Wi-Fi throughout the property, and treat yourself to some well-deserved pampering at our massage spa. We look forward to making your stay enjoyable and memorable!

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Boutique hotel amenities:

Wellness Facilities • Child Friendly • Transportation/Shuttle • Skiing

boutique hotels in Japan
Hotel
600-8126 Kyoto, Kyoto, Shimogyo-ku Kagiya cho 342, Japan

Marufukuro is a welcoming place to stay in Kyoto, offering a beautiful garden, a cozy lounge, and a lovely terrace for guests to enjoy. There's also a restaurant on-site where you can savor delicious meals. If you’re looking to explore, you’ll find several popular attractions nearby, like the TKP Garden City Kyoto, which is just about a 15-minute walk away. Whether you're here for relaxation or adventure, Marufukuro aims to provide a comfortable and enjoyable experience for everyone.

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Boutique hotel amenities:

Child Friendly • Entertainment • Wellness Facilities • Restaurant • Spa • Sports/Activities

boutique hotels in Japan
Hotel
506-1434 Gifu, Takayama, Okuhida Onsengo Fukuchi 10, Japan

Welcome to Katsuragi no Sato, a charming retreat nestled in the serene Okuhida hot-spring area. Here, you can relax in our spacious Japanese-style cottages, designed for your comfort and enjoyment. Each cottage features free Wi-Fi, cozy tatami (woven-straw) floors, and a traditional Irori hearth that adds warmth and character to your stay. Whether you prefer indoor or outdoor experiences, our peaceful surroundings invite you to unwind and connect with nature. We’re dedicated to ensuring your visit is enjoyable and fulfilling. Come and create lasting memories with us!

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Boutique hotel amenities:

Restaurant • Wellness Facilities • Hot Tub • Entertainment • Spa • Child Friendly • Sports/Activities

boutique hotels in Japan
Hotel
605-0074 Kyoto, Kyoto, Higashiyama-ku Gionmachi Minamigawa 570-89, Japan

Welcome to Hotel Gion Ichirin, conveniently located in beautiful Kyoto, just a short 800 meters from Gion Shijo Station. We’re here to make your stay comfortable and enjoyable! Our hotel features cozy, non-smoking rooms and a welcoming shared lounge where you can relax and connect with fellow guests. Plus, we offer free WiFi throughout the property so you can stay connected with loved ones or plan your next adventure. If you need assistance with your luggage, our friendly staff is always happy to help. We look forward to making your experience in Kyoto memorable!

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Boutique hotel amenities:

Entertainment • Wellness Facilities • Spa

boutique hotels in Japan
Hotel
604-0003 Kyoto, Kyoto, Nakagyo-ku Hanatatecho 255-1, Japan

Welcome to Nazuna Kyoto Gosho, your cozy retreat in the heart of Kyoto! We’re excited to offer you complimentary WiFi so you can stay connected during your visit. Our location is conveniently close to some amazing attractions: just a short walk away, you’ll find the Kyoto International Manga Museum, Nijo Castle, and the beautiful Kyoto Imperial Palace, all within 1.3 kilometers. We hope you enjoy your stay with us and explore the rich culture and history that Kyoto has to offer!

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Boutique hotel amenities:

Restaurant • Wellness Facilities • Hot Tub • Entertainment

boutique hotels in Japan
Hotel
506-1434 Gifu, Takayama, Okuhidaonsenkyo Fukuchi 687, Japan

Welcome to Hidaji, a peaceful retreat in the beautiful Northern Alps. Here, you can enjoy spacious accommodations designed in the traditional Japanese style, surrounded by stunning natural scenery. We prioritize your comfort and relaxation, so feel free to ask about our massage services during your stay. We’re here to help you unwind and connect with nature.

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Boutique hotel amenities:

Transportation/Shuttle • Sports/Activities • Hot Tub • Wellness Facilities • Entertainment

boutique hotels in Japan
Hotel
111-0032 Tokyo-to, Taitoku Asakusa 3-32-12, Japan

Located in the vibrant city of Tokyo, just a short 300-meter walk from the beautiful Asakusa Fujiasama Shrine and about 7.5 kilometers from the bustling city center, cyashitsu ryokan asakusa offers a welcoming retreat. Our comfortable rooms are equipped with air conditioning and free WiFi to ensure you feel at home during your stay. You can also unwind and relax in our serene open-air bath, providing a perfect space for rejuvenation. We strive to create an inclusive and relaxing environment for all our guests, making your experience with us truly special.

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Boutique hotel amenities:

Hot Tub • Child Friendly • Entertainment • Restaurant • Wellness Facilities

boutique hotels in Japan
Hotel
739-0454 Hiroshima, Hatsukaichi, Miyahamaonsen 3-5-27, Japan

Experience the warmth of Japanese hospitality at Sekitei, nestled in the beautiful Miyahama hot-spring area. Our spacious accommodations reflect traditional Japanese design, offering a comfortable and inviting atmosphere for all guests. Stay connected with free Wi-Fi throughout your visit. Take some time to unwind in our soothing hot-spring baths, where you can relax and rejuvenate while enjoying the stunning sea views. We strive to create a welcoming environment that caters to everyone, ensuring you have a memorable stay with us.

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Boutique hotel amenities:

Child Friendly • Spa • Wellness Facilities • Transportation/Shuttle • Sports/Activities • Restaurant • Entertainment • Hot Tub

boutique hotels in Japan
Hotel
847-0017 Saga, Karatsu, Higashi Karatsu 2-4-40, Japan

Yoyokaku is a welcoming place to stay in Karatsu, located less than a kilometer from the beautiful Nishinohama Beach. Here, you can enjoy complimentary bicycles for easy exploration of the area, relax in the peaceful garden, and benefit from helpful housekeeping services to make your stay more comfortable. This cozy ryokan offers a friendly atmosphere and thoughtful amenities to cater to your needs. Whether you’re seeking adventure or tranquility, Yoyokaku is a great choice for your visit.

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Boutique hotel amenities:

Transportation/Shuttle • Business Services • Entertainment • Child Friendly

boutique hotels in Japan
Hotel
604-8174 Kyoto, Kyoto, Nakagyo-ku Ennogyojacho 375, Japan

Villa Sanjomuromachi KYOTO opened its doors in July 2016, just a short 5-minute stroll from the Karasuma Oike Subway Station, which connects to both the Karasuma and Tozai Lines. We invite you to experience a peaceful stay in our welcoming accommodations, designed with your comfort in mind. Whether you're traveling for leisure or work, we are here to make your visit enjoyable and memorable.

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Boutique hotel amenities:

Entertainment • Wellness Facilities • Child Friendly

boutique hotels in Japan
Hotel
669-6101 Hyogo, Toyooka, Kinosaki-cho Yushima 844, Japan

Yuraku Kinosaki Spa & Gardens offers a welcoming experience in the beautiful Kinosaki hot-spring area, known for its traditional Japanese charm. Here, you can unwind in both indoor and outdoor hot-spring baths, enjoying the soothing waters that have made this location famous. Whether you prefer to soak indoors or enjoy the fresh air outside, there’s a perfect spot for everyone to relax and rejuvenate. Come and experience the serene atmosphere and the warmth of Japanese hospitality.

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Boutique hotel amenities:

Spa • Hot Tub • Child Friendly • Transportation/Shuttle • Wellness Facilities

boutique hotels in Japan
Hotel
509-4241 Gifu, Hida, Furukawa Mukaimachi 1-8-27, Japan

Yatsusankan provides a warm and welcoming Japanese-style lodging experience, complete with roomy public baths for relaxation. Conveniently located just a 6-minute stroll from JR Hidafurukawa Train Station, it’s easy to access. Guests can enjoy complimentary WiFi in the common areas, helping you stay connected during your stay. We aim to create a comfortable environment for everyone, making your visit as enjoyable as possible.

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Boutique hotel amenities:

Entertainment • Wellness Facilities • Restaurant • Skiing • Business Services • Spa • Sports/Activities • Transportation/Shuttle

boutique hotels in Japan
Hotel
250-0521 Kanagawa, Hakone, Hakone 521, Japan

Nestled among serene bamboo trees and gentle hills, Yoshimatsu is a welcoming traditional inn, known as a Ryokan, that offers a warm and authentic experience. Guests can enjoy soothing outdoor hot spring baths while taking in breathtaking views of Mt. Fuji and Lake Ashi. To make your stay even more enjoyable, we provide a complimentary shuttle service to help you get around easily. We look forward to welcoming you!

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Boutique hotel amenities:

Entertainment • Wellness Facilities • Hot Tub • Sports/Activities

boutique hotels in Japan
Hotel
605-0907 Kyoto, Kyoto, Higashiyama-ku Tonya-machidori-gojosagaru 3 Nishitachibana 467, Japan

Seikoro Ryokan is a welcoming place to stay in Kyoto, just a short 7-minute drive from JR Kyoto Station. Here, you can experience the charm of traditional Japanese-style accommodations. The ryokan features a relaxing public bath where you can unwind, as well as massage services to help you feel at ease. Plus, you’ll have access to free Wi-Fi, making it easy to stay connected during your visit. We look forward to making your stay comfortable and enjoyable!

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Boutique hotel amenities:

Wellness Facilities • Entertainment • Child Friendly

boutique hotels in Japan
Hotel
606-8435 Kyoto, Kyoto, Sakyo-ku, Nanzenji Fukuchi-cho 31, Japan

If you're looking for a welcoming place to stay in Kyoto, consider Nanzenji sando KIKUSUI, which is conveniently located just 1.1 km from the beautiful Shoren-in Temple. Our accommodations offer easy access to a lovely garden and a shared lounge where you can relax and connect with others. We also have a lift to ensure everyone can move around comfortably. We aim to create a friendly environment that feels like home during your visit.

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Boutique hotel amenities:

Child Friendly • Restaurant • Entertainment

Most booked boutique hotels in Japan

boutique hotels in Japan
605-0907 Kyoto, Kyoto, Higashiyama-ku Tonya-machidori-gojosagaru 3 Nishitachibana 467, Japan
9.6
797 reviews
From $424
boutique hotels in Japan
111-0032 Tokyo-to, Taitoku Asakusa 3-32-12, Japan
9.6
428 reviews
From $413
boutique hotels in Japan
250-0521 Kanagawa, Hakone, Hakone 521, Japan
9.7
340 reviews
From $549.64

Budget boutique hotels in Japan

boutique hotels in Japan
602-8252 Kyoto, Kyoto, Kamigyo-ku Kamichojamachi Kitakodaimoncho 548-1, Japan
9.9
305 reviews
From $143.64
boutique hotels in Japan
044-0081 Hokkaido, Kutchan, Yamada 170-248, Japan
9.8
40 reviews
From $149
boutique hotels in Japan
605-0074 Kyoto, Kyoto, Higashiyama-ku Gionmachi Minamigawa 570-89, Japan
9.5
133 reviews
From $182.02

Compare the Best Boutique Hotels in Japan – Addresses, Prices, Stars, Rating, and Review Count

Hotel Name Address Price ($) Star Rating Review Count Book
Seizan Yamato 414-0055 Shizuoka, Ito, Oka 203 , Japan 504 4 10 1
Genji Kyoto, a Member of Design Hotels 600-8113 Kyoto, Kyoto, Hashidono-cho 362-3, Shimogyo-ku, Japan 239 4 9.7 212
Snowball Chalet at Madarao Mountain 389-2253 Nagano, Iiyama, Iiyama 11492-331, Japan 638.8 3 9.9 9
Ryokan Mugen (Adult Only) 602-8252 Kyoto, Kyoto, Kamigyo-ku Kamichojamachi Kitakodaimoncho 548-1, Japan 143.64 4 9.9 305
Onpoint Madarao 949-2223 Niigata, Myoko, Tarumoto 1101-215, Japan 230 3 9.6 25
Kimamaya By Odin 044-0081 Hokkaido, Kutchan, Yamada 170-248, Japan 149 3 9.8 40
Marufukuro 600-8126 Kyoto, Kyoto, Shimogyo-ku Kagiya cho 342, Japan 616 5 9.6 296
Katsuragi no Sato 506-1434 Gifu, Takayama, Okuhida Onsengo Fukuchi 10, Japan 462.96 4 9.8 38
Hotel Gion Ichirin 605-0074 Kyoto, Kyoto, Higashiyama-ku Gionmachi Minamigawa 570-89, Japan 182.02 3 9.5 133
Nazuna Kyoto Gosho 604-0003 Kyoto, Kyoto, Nakagyo-ku Hanatatecho 255-1, Japan 1253 4 9.6 81
Hidaji (Adult Only) 506-1434 Gifu, Takayama, Okuhidaonsenkyo Fukuchi 687, Japan 517 4 9.7 185
cyashitsu ryokan asakusa 111-0032 Tokyo-to, Taitoku Asakusa 3-32-12, Japan 413 3 9.6 428
Sekitei 739-0454 Hiroshima, Hatsukaichi, Miyahamaonsen 3-5-27, Japan 684.16 5 0 0
Yoyokaku 847-0017 Saga, Karatsu, Higashi Karatsu 2-4-40, Japan 192 3 9.6 247
Villa Sanjomuromachi KYOTO 604-8174 Kyoto, Kyoto, Nakagyo-ku Ennogyojacho 375, Japan 455 5 9.4 160
Yuraku Kinosaki Spa & Gardens 669-6101 Hyogo, Toyooka, Kinosaki-cho Yushima 844, Japan 260.56 4 9.7 57
Yatsusankan 509-4241 Gifu, Hida, Furukawa Mukaimachi 1-8-27, Japan 255 5 9.6 242
Yoshimatsu 250-0521 Kanagawa, Hakone, Hakone 521, Japan 549.64 4 9.7 340
Seikoro Ryokan - Established in 1831 605-0907 Kyoto, Kyoto, Higashiyama-ku Tonya-machidori-gojosagaru 3 Nishitachibana 467, Japan 424 4 9.6 797
Nanzenji sando KIKUSUI 606-8435 Kyoto, Kyoto, Sakyo-ku, Nanzenji Fukuchi-cho 31, Japan 973 3 9.5 68

Note: The prices for each boutique hotels in Japan do vary. This can be because of the number of people you are booking for, how far in advance you book and the season. The prices above are only meant as a rough estimate for comparison purposes. Click the buttons above (or click here>) to get the latest prices.

Top 8 Attractions in Japan, Japan

Luxury Shopping in Ginza: Experience world-class shopping in Ginza, where you can find everything from high-end fashion boutiques to exquisite art galleries, making it an ideal place to indulge after a day of exploring your luxury or boutique stay in Japan, Japan.

Historic Kyoto Temples: Immerse yourself in the serene beauty of Kyoto’s historic temples, such as Kinkaku-ji and Fushimi Inari Taisha, which provide a stunning backdrop for a peaceful retreat near your boutique accommodation.

Mount Fuji: Climb or admire the iconic Mount Fuji, Japan's tallest peak, known for its breathtaking views that complement the tranquil atmosphere surrounding your luxury stay in Japan, Japan.

Hiroshima Peace Memorial Park: Visit the poignant Hiroshima Peace Memorial Park, a tribute to the resilience of humanity, offering a profound experience just a short journey from boutique hotels in the area.

Tokyo Skytree: Ascend the Tokyo Skytree for unparalleled panoramic views of the city skyline, providing a thrilling contrast to the cozy charm of your luxury or boutique stay in Japan, Japan.

Okinawa Beaches: Relax on the pristine beaches of Okinawa, famous for their crystal-clear waters and vibrant marine life, perfect for unwinding after a day spent enjoying your boutique hotel amenities.

Historic Nara: Explore Nara, home to friendly free-roaming deer and significant cultural treasures like Todai-ji Temple, which adds a historical dimension to your elegant escape near your luxury accommodation.

Sapporo Snow Festival: If your travels coincide with winter, don’t miss the Sapporo Snow Festival, celebrated annually with dazzling ice sculptures and snow activities, enhancing the allure of your boutique stay in Japan, Japan.

Frequently Asked Questions

Transportation/Shuttle service is available at the following boutique hotels in Japan:

  • Snowball Chalet at Madarao Mountain.- Review Count: 9, Rating: 9.9
  • Kimamaya By Odin.- Review Count: 40, Rating: 9.8
  • Hidaji (Adult Only).- Review Count: 185, Rating: 9.7

A spa is available to guests at the following boutique hotels in Japan:

  • Marufukuro.- Review Count: 296, Rating: 9.6
  • Katsuragi no Sato.- Review Count: 38, Rating: 9.8
  • Hotel Gion Ichirin.- Review Count: 133, Rating: 9.5

Families traveling in Japan enjoyed their stay at the following boutique hotels:

  • Seizan Yamato.- Review Count: 1, Rating: 10
  • Genji Kyoto, a Member of Design Hotels.- Review Count: 212, Rating: 9.7
  • Snowball Chalet at Madarao Mountain.- Review Count: 9, Rating: 9.9

These 3 star hotels received great reviews from other travelers:

  • Snowball Chalet at Madarao Mountain.- Review Count: 9, Rating: 9.9
  • Onpoint Madarao.- Review Count: 25, Rating: 9.6
  • Kimamaya By Odin.- Review Count: 40, Rating: 9.8

Some of the best boutique hotels in Japan are:

  • Marufukuro.- Review Count: 296, Rating: 9.6
  • Yatsusankan.- Review Count: 242, Rating: 9.6
  • Villa Sanjomuromachi KYOTO.- Review Count: 160, Rating: 9.4