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Boutique Hotels in San Francisco: Nine of the Best in the City

Staying at one of the boutique hotels in San Francisco is a great SF lodging alternative. Here you will find 9 of the best options, from bed and breakfasts to small, personal hotels.

Many of the recommendations on this list are in local neighborhoods yet still close to the main SF attractions and activities. Staying at a boutique hotel in San Francisco is the perfect way to get an authentic SF experience.

Disclaimer: I receive a small commission from some of the links on this page.

1. Inn at the Presidio

Boutique Hotels in San Francisco

Address: 42 Moraga Avenue

Nightly Rates: From around $330 - $545

Number of Rooms: 22

Neighborhood: Presidio

This newly opened inn is situated inside the San Francisco Presidio, a National Historic Landmark. You will find large, quiet rooms in remodeled army officers' quarters here.

Of the 22 rooms, 17 are suites with a gas fireplace and a sofa sleeper. The hotel also features an outdoor patio with a gas fire pit, porches with rocking chairs, and large public lobbies.

Amenities here include:

  • Free WiFi throughout the hotel
  • Complimentary Continental breakfast
  • Daily morning newspaper
  • Affordable and convenient parking (around $8 a day)
  • Afternoon wine and cheese receptions
  • Pet Friendly ($40 fee)

The hotel also provides free shuttles to get around the Presidio (which contains attractions like the Disney Museum, Officer's Club, and more), as well as to and from the Golden Gate Bridge and downtown.

You can also take a pleasant walk or public transportation from the hotel to get to Baker Beach, Crissy Field, Fisherman's Wharf, Union Square, and other popular areas.

>> Compare online prices and read recent guest reviews for the Inn at the Presidio on TripAdvisor.

2. Union Street Inn

Address: 2229 Union Street

Nightly Rates: Range from $219 - $329

Number of Rooms: 6

Neighborhood: Marina District

The most requested boutique hotel in San Francisco is the Union Street Inn. This small bed and breakfast is located on Union Street, where you will find many cute shops, restaurants, and wine bars.

It's about a 15-minute walk to Fisherman's Wharf, a 10-minute walk to the Presidio, and only about a 10-minute walk to the waterfront. This neighborhood also has good public transportation, so you can easily take the bus to see other key neighborhoods and top sights.

Guests absolutely love this place, especially the charm, hospitality, and pampering touches, like fresh fruit in the rooms and wine and cheese receptions every afternoon.

Here are some of the additional amenities at the Union Street Inn:

  • Breakfast included
  • Free high-speed internet
  • Suites available
  • Air conditioning
  • Quaint backyard garden
  • Bridal Suite

>> Read what other travelers have to say about the Union Street Inn and find booking details on TripAdvisor. Note: You will have to call the Union Street Inn to book rooms because they are so limited.

3. Queen Anne Hotel

Japantown HotelsThe Peace Pagoda in the Japantown District

Address: 1590 Sutter Street

Nightly Rates: From $186 - $489

Number of Rooms: 48

Neighborhood: Pacific Heights/Japantown

The Queen Anne Hotel is one of the larger boutique hotels in San Francisco. Set in the beautiful Pacific Heights neighborhood, this historic, Victorian-style building that dates back to 1890 sits proudly on the corner of Sutter and Octavia.

Inside, you'll find charming accommodations with stained glass windows and antiques throughout. Each room is individually decorated with Victorian pieces, which adds to the hotel's character.

Amenities at the Queen Anne Hotel include:

  • Free continental breakfast
  • Free wireless internet access
  • Business center
  • Cable/satellite TVs
  • Room service
  • Dry Cleaning and laundry service
  • Limo or town car service for a small fee

Discounted access to three health clubs within a few blocks of the hotel

>> Discover recent guest reviews and the best deals for your stay at the Queen Anne Hotel on TripAdvisor.

4. The Inn San Francisco

Address: 943 South Van Ness

Nightly Rates: Range from $235 - $415

Number of Rooms: 21

Neighborhood: Mission District

Another exciting option for boutique hotels in San Francisco is The Inn San Francisco in the Mission District. This small bed and breakfast is warm and inviting.

You are sure to feel at home with a quiet outdoor garden, a gorgeous rooftop terrace, and cozy fireplaces. You will also be close to some of the best restaurants and bars in the city.

Other amenities at this bed and breakfast include:

  • Free breakfast buffet
  • Free high-speed internet
  • Hot tub in the garden
  • Panoramic views from the rooftop
  • Shared or private bathrooms available
  • Individually decorated rooms
  • Refrigerator and TV in room
  • Pet Friendly

If you are a light sleeper, make sure you check the noise level of your room before booking. Some rooms are just steps off noisy Van Ness Street, but there are also several quieter options in the back.

>> Find more tips from recent guests and compare prices for The Inn San Francisco on TripAdvisor.

5. The Parsonage

Civic Center HotelsA look at City Hall and a memorial in the Civic Center District.

Address: 198 Haight Street

Nightly Rates: From about $260 - $368

Number of Rooms: 5

Neighborhood: Civic Center/Hayes Valley

Another one of my favorite boutique hotels in San Francisco is The Parsonage. This bed and breakfast is located in one of the hottest San Francisco neighborhoods, where new bars and restaurants are opening up daily. You are also within walking distance of San Francisco's subway system, BART.

Rooms at The Parsonage are comfortable and quiet. The owners take great care of both their property and their guests, so you will surely have a great experience here.

Amenities at The Parsonage include:

  • Amazing multi-course seasonal complimentary breakfast
  • Free high-speed internet access
  • Queen beds with superior linens
  • Marble showers
  • Fireplaces and/or views from all the rooms
  • Powered 100% by renewable electricity

>> Read recent guest reviews for The Parsonage on TripAdvisor. Note they require a two-day minimum.

Other Great Boutique Hotels San Francisco

Rainbow Flag in Harvey Milk Plaza in the Castro DistrictRainbow Flag in Harvey Milk Plaza in the Castro District

6. Parker Guest House: 520 Church Street, Castro/Mission neighborhoods

  • Cute bed and breakfast located between the Castro and Mission neighborhoods
  • Free breakfast, library, free high-speed internet, and personalized service
  • 21 rooms
  • Rooms start at around $209 - $299 a night

>> Find out more about the Parker Guest House and rooms

7. The Metro Hotel: 319 Divisadero Street, Alamo Square neighborhood

  • Central location near the Haight-Ashbury District and Golden Gate Park
  • Free high-speed internet access
  • Beautiful private garden courtyard only for hotel guests
  • 24 rooms
  • Rooms from $230 - $355 a night

>> Get the best deals for your stay at The Metro Hotel

8. Golden Gate Hotel: 755 Bush Street, Lower Nob Hill

  • Charming, centrally located bed and breakfast with antique décor
  • Resident cat, Pip, roaming freely around the hotel
  • Parking available for $35 a day
  • Breakfast included
  • 25 rooms
  • Rooms for about $199 - $269 a night
  • NOTE: Depending on the date, they may require a three-day reservation

>> Learn about the Golden Gate Hotel and find your choice of rooms

9. Phoenix Hotel: 601 Eddy Street, Civic Center neighborhood

  • Recently remodeled hotel targeting a young, art loving crowd (many traveling bands like to stay here due to its location and funky vibe)
  • Bar/lounge and restaurant on site
  • Free high speed internet, breakfast and parking
  • Outdoor swimming pool
  • 44 rooms
  • Rooms from $214 - $335 a night
  • >> Find out more about the Phoenix Hotel and rooms for your vacation

Find the best deal, compare prices, and read what other travelers have to say about these and other boutique hotels in San Francisco on TripAdvisor.

Other SF Hotel Options

BookingFind great deals all around San Francisco for your upcoming stay

TripAdvisorWhat's the #1 hotel in San Francisco? Read reviews & find hotel deals on TripAdvisor!

VRBO: In addition to hotels, you'll also find some great places to stay locally through VRBO. Book an apartment or a room and feel more like a local. Find some great places to stay on VRBO here

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