
Boutique hotels in Shinjuku
Find and book unique boutique hotels on Airbnb
Quick stats about boutique hotels in Shinjuku

Total vacation rentals
Explore 30 vacation rentals in Shinjuku

Nightly prices starting at
Shinjuku vacation rentals start at $40 per night before taxes and fees

Verified guest reviews
Over 4,750 verified reviews to help you choose

Rentals with dedicated workspaces
10 properties have a dedicated workspace

Wi-Fi availability
30 of Shinjuku vacation rentals include wi-fi access

Popular amenities for guests
Guests love Kitchen, Wifi, and Pool across Shinjuku rentals

4.7 Average rating
Shinjuku stays receive an average rating of 4.7 out of 5 from guests

Nearby attractions
Shinjuku's top spots, include Shinjuku Gyoen National Garden, Sunshine Aquarium, and Tokyo Metropolitan Theatre
Top-rated boutique hotels in Shinjuku
Guests agree: these boutique hotels are highly rated for location, cleanliness, and more.

The Hideout Tokyo -(Double Room)-
We're Central Tokyo's family run hotel for those who want to travel in style. Our petite 5-room hotel offers reasonably priced compact yet cozy accommodation with many of the features you'd expect from a larger,branded property. Private shower&sink. We're located walking distance from many of Tokyo's finest sightseeing spots and just a 4/2 minute walk from JR Yamanote line,Subway Hibiya line connecting you quickly to the rest of the city. ※We’re legal hotel with hotel permit from the government
ValueLocationBathroom

DOMO HOTEL-1
DOMO HOTEL is located in the Shinjuku area, within walking distance of JR Shin-Okubo Station and Shinjuku Station. A convenience store can be reached in 30 seconds. There are many chain restaurants, cafes, post offices and drug stores around the hotel, taking care of the needs of tourists in every possible way. In order to provide travelers with a brand-new accommodation experience, the hotel has only 12 rooms. From the moment you step into the hotel door, an unprecedented journey begins quietly
ValueLocationAir conditioning

Standard Room|Accessible|20mShinjuku|Kagurazaka
Barrier-free room ideal for families or small groups. The ground-floor 30 m² twin sleeps up to 4 with two Simmons double beds. In-room: free Wi-Fi, A/C, mini-fridge, air-purifier, safe, TV and hair-dryer. Bathroom stocked with shampoo, conditioner, body & hand soap, towels, gowns, slippers, toothbrush set, cotton kit, razor, sponge and brush. No on-site parking or washer—please use nearby coin lots and laundromats. Fee-based rentals (limited): hair iron, board games, projector, Fire TV Stick.
ValueFamilyCheckout

④2020年新築貸切/クイーンベッド/モダンバスルーム/Rain showerサンシャインシティ3分
Newly built with travelers in mind. The rooms are spacious with Queen size beds (practically unheard-of in Japan). Smart TV, Wi-Fi, tea and coffee. The bathrooms are fashionable, with large walk in rain showers. LED mirrors to get you ready for whatever lighting you will encounter. Rooms have a bar fridge, microwave and kettle for you to store and prepare ready-made meals and drinks. All rooms come equipped with Air-conditioning, ceiling fans and black-out curtains. Ample storage space also!
ValueFamilyAccess

Luxury Art Penthouse | Tokyo Bay Ocean View |10pax
Welcome to Art House 日の出, one-of-a-kind penthouse overlooking spectacular Tokyo Bay.Created by visionary creators and architects, this top-floor private residence, which blends contemporary art with traditional Japanese aesthetics, just opened in January 2026 as an immersive space.This entire 87㎡ floor is reserved exclusively for your family, group of friends (up to 10 guests). Designed as a “Art Gallery Hotel” offers a premium, memorable stay beyond the ordinary accommodation experience.
ValueFamilySleep quality

12-min walk to Sensoji - Boutique Hotel
一遊ホテル浅草 is a boutique hotel located in Taito City, offering excellent access to major transportation. Nestled in a quiet residential neighborhood, yet close to Tokyo’s most popular sightseeing spots, this is an ideal base for tourists, couples, and business travelers – only a 12-minute walk from the famous Sensoji Temple, where you can enjoy the blend of traditional culture and modern Tokyo vibes. Plenty of dining options nearby, from traditional Japanese food to stylish cafes.
LocationValueLaundry

Hotel Suite | 7 min JR Shin-Okubo | 4 min Subway
I GO HOTEL is in central Shinjuku, a 3-minute walk to Higashi-Shinjuku Station (Fukutoshin Line, Exit B1) and 5 minutes to the Oedo Line, with direct access to Shibuya, Harajuku, Ikebukuro, and Roppongi. Shin-Okubo Station, Seibu-Shinjuku Station, Okubo Station, and Shinjuku Station are within walking distance. Near Kabukicho and Shin-Okubo, with 24-hour convenience stores, restaurants, drugstores, and Don Quijote nearby. Central yet quiet.
LocationValueAmenities

3 min to Sensoji | Skytree View | 2BR Family Apt
Opened in the summer of 2021, this apartment hotel was designed by a well-known Japanese designer. The building has 9 floors and 16 Quad rooms, ideal for families or small groups of 4–5 guests. The hotel is located along the main road near Senso-ji Temple and Asakusa Shrine. Front desk hours: 10:00 AM – 8:00 PM Online customer support: 8:00 PM – 12:00 AM Late-night front desk service: 10:00 PM – 6:00 AM (available on five nights per week)
FamilyLocationComfort

1 min from Koenji Station/BnA Koenji Room 2F
BnA Home Koenji is an independent art hotel created by the Bed & Art Project (BnA)—an ambitious and experimental hospitality concept that blends art, community, and immersive travel. At BnA, guests don't just stay at a hotel—they stay inside a work of art. Each room is a one-of-a-kind collaboration, designed and built by local artists, architects, textile designers, and carpenters to create a deeply personal and unforgettable experience.
LocationValueCheck-in

Tabiji Shibuya |10 min Walk from Shibuya sta
Very popular property – early booking recommended. Private full-floor stay in a quiet area, just a 10-minute walk from Shibuya Station. Comfortable, stylish, and ideal for families or groups. Located on the 5th floors with elevator access. Sleeps up to 10guests with 4 double beds and 1 king bed, all with Koala mattresses. Includes 2 shower rooms, kitchenware, washer-dryer, record player, Bluetooth speaker, and projector. No TV.
FamilyLocationSleep quality

TheMillennialsShibuya/Mixed Smart Pod/1 Guest
Welcome to The Millennials Shibuya, a futuristic accommodation facility equipped with the world's first IOT-equipped "Smart Pod" and a lounge with a coworking space. In addition, there are plenty of common spaces, including a 24-hour shared lounge, a 24-hour self-kitchen, a 24-hour working lounge, a shared shower and toilet, and a shared laundry. 20% of the total area of the hotel is allocated to the common area.
ValueLocationBreakfast

PEGASUS HOTEL (Western Style room) 201
Hi This is Pegasus Hotel New open in 2020, we have two types of standard double rooms and family rooms. The environment is clean and tidy. It is a three-minute walk from Asakusa Bridge Station. , Every year will have Sumidagawa Fireworks Festival, Japanese traditional culture boat house you also can have a nice dinner in the boat, you can have a good time in nearby Tokyo Bay Odaiba Rainbow Bridge, etc.
FamilyLocationComfort
Popular amenities for Shinjuku boutique hotels
Family-friendly boutique hotels

condominium with everything you need for dailylife
ValueLocationAccuracy

【IKOI_403】Well-Equipped Hidden Gem: Hibiya Line
ValueLocationWifi

Newly opened hotel-style t suite Subway 3 minutes
ValueLocationIndoor spaces

New hotel/Deluxe double/2 people
ValueLocationQuiet

3 mins to Subway | Rare Triple Room | Balcony
ValueLocationAir conditioning

No Service Hotel 301 / 7 min to Asakusa
LocationHospitalityCleanliness

4 subway 5 min walk! Japanese style Tatami&Futon
FamilyLocationHospitality

Japanese Ryokan | Ueno/Akihabara | 10 Guests OK
LocationValueAir conditioning
Boutique hotels with a patio

Washing Machine, Apartment Suite, 5 Min Walk to Skytree Station, Direct Access to Airport, Kitchen, Nearby Izakaya, Amin Hotel
LocationValueCleanliness

8 min to Yamanote Line | 3BR Family Suite | 49㎡
FamilyLocationCleanliness

TheMillennialsShibuya/Smart Pod Girls Only/1 Guest
ValueLocationAccess

5 min walk to Skytree Station, direct access to airport and Disney, kitchen, washing machine, wifi, elevator, Amin Hotel
LocationViewIndoor spaces

5 min walk to Skytree Station, 100 inch projection screen in the movie room, direct access to the airport, kitchen, washing machine, bathtub
ValueLocationAccuracy
Other boutique hotel vacation rentals

Tokyo Home near Disney for 2|Cozy Room|Kitchen
LocationValueAmenities

Room 201, 3 mins walk from Asakusabashi Station, Asakusa, Akihabara, Ueno neighborhood, kitchenware, kitchen, washing machine, direct access to Haneda and Narita Airport
LocationValueIndoor spaces

Economy Double Room with Sofa Bed Max4 Comfort2
ValueLocationAccess

Direct to Shinjuku|3min Sugamo|Shop St|WiFi|2pax
ValueLocationCheck-in

[1]2min walk Sta丨Shinjuku area丨free WIFI丨Single丨
ValueLocationAmenities

4 single beds in Tokyo/2 train stations: Studio B
FamilyValueAir conditioning

3 mins to Subway | Rare Triple Room | Balcony
ValueLocationAmenities

Newly opened hotel-style t suite Subway 3 minutes
ValueLocationKitchen
When is the best time to visit Shinjuku?
| Month | Jan | Feb | Mar | Apr | May | Jun | Jul | Aug | Sep | Oct | Nov | Dec |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Avg. price | $91 | $90 | $97 | $104 | $81 | $71 | $87 | $72 | $107 | $109 | $110 | $98 |
| Avg. temp | 42°F | 44°F | 49°F | 58°F | 66°F | 72°F | 79°F | 81°F | 75°F | 65°F | 55°F | 46°F |
Destinations to explore
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- Boutique hotels Tokyo Prefecture
- Boutique hotels Japan
- Tokyo Sta.
- Shibuya Station
- Tokyo Disneyland
- Asakusa Sta.
- Akihabara Sta.
- Shimo-Kitazawa Sta.
- Ikebukuro
- Tokyo Disney Resort
- Tokyo Skytree
- Nippori Sta.
- Ueno Sta.
- Yokohama Sta.
- Oshiage Sta.
- Takadanobaba Sta.
- Tokyo Tower
- Kinshicho Sta.
- Hakone-Yumoto Sta.
- Kita-Senju Sta.
- Shinagawa
- Yoyogi Park
- Omiya Sta.
- Tokyo Dome
- Akabane Sta.
- Gotanda Sta.
- Things to do Shinjuku
- Art and culture Shinjuku
- Tours Shinjuku
- Nature and outdoors Shinjuku
- Sightseeing Shinjuku
- Entertainment Shinjuku
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- Food and drink Shinjuku
- Things to do Tokyo Prefecture
- Nature and outdoors Tokyo Prefecture
- Sightseeing Tokyo Prefecture
- Tours Tokyo Prefecture
- Entertainment Tokyo Prefecture
- Sports activities Tokyo Prefecture
- Food and drink Tokyo Prefecture
- Wellness Tokyo Prefecture
- Art and culture Tokyo Prefecture
- Things to do Japan
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- Family travel hub Tips and inspiration
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