Beginning of main content
Trip Type
Flight 1
Flight 2
Flight 3
Flight 4
Flight 5

Search 321,000 hotels worldwide.

Get the best price available for your trip.

No Expedia cancellation fee to change or cancel almost any hotel reservation.


Featured San Rafael Independent Hotels

See all 639 Hotels in San Rafael
Hotel Whitcomb

Hotel Whitcomb

1231 Market St, San Francisco
3.5 out of 5.0
3.3 out of 5 (8,237 reviews)
Decent Hotel I have stayed here a dozen times in the past 3 years. It’s affordable and provides a nice place to … - 

$105

$105
Hotel Zoe San Francisco

Hotel Zoe San Francisco

425 North Point, San Francisco
4.0 out of 5.0
4.2 out of 5 (5,636 reviews)
Great STAFF - competitive rates - LOVE LOVE LOVE the location - 

$149

$149
Sheraton Fisherman's Wharf Hotel

Sheraton Fisherman's Wharf Hotel

2500 Mason St, San Francisco
4.0 out of 5.0
3.8 out of 5 (3,921 reviews)
Nice hotel It was confortable and very clean! Close to the beach and many attractions - 

$149

$149
Clift

Clift

495 Geary St, San Francisco
4.5 out of 5.0
4.1 out of 5 (3,443 reviews)
Clean but needs to join the digital age. No charging ports, broken floor lamp switch, extra “facility charge” that reeks of extra add-on air … - 

$159

$159
Hotel Nikko San Francisco

Hotel Nikko San Francisco

222 Mason St, San Francisco
4.5 out of 5.0
4.3 out of 5 (6,520 reviews)
Great central location Exceptionally friendly and competent staff from doorman to person delivering bottle opener promptly … - 

$157

$157
Hyatt Regency San Francisco

Hyatt Regency San Francisco

5 Embarcadero Center, San Francisco
4.0 out of 5.0
4.3 out of 5 (3,168 reviews)
Andy at ceck in provided World class service to me andy family - 

$159

$159
The Westin St. Francis San Francisco on Union Square

The Westin St. Francis San Francisco on Union Square

335 Powell Street, San Francisco
4.5 out of 5.0
4.2 out of 5 (4,374 reviews)
Very Beautiful Hotel Perfect Location. Wonderful views. Outstanding service. - 

$158

$158
Palace Hotel, a Luxury Collection Hotel, San Francisco

Palace Hotel, a Luxury Collection Hotel, San Francisco

2 New Montgomery St, San Francisco
5.0 out of 5.0
4.5 out of 5 (3,030 reviews)
Comfortable hotel I love staying at the Palace Hotel. The beds and pillows are so comfortable and the rooms are spaci … - 

$167

$167
Pier 2620 Hotel Fisherman's Wharf

Pier 2620 Hotel Fisherman's Wharf

2620 Jones Street, San Francisco
4.0 out of 5.0
4.2 out of 5 (4,088 reviews)
We will definitely be back! Bill was absolutely wonderful checking us in. This is our second time here and definitely will not … - 

$161

$161
Holiday Inn San Francisco-Fisherman's Wharf

Holiday Inn San Francisco-Fisherman's Wharf

1300 Columbus Ave, San Francisco
3.5 out of 5.0
3.9 out of 5 (4,991 reviews)
Close to the wharf The hotel is within walking distance of Fisherman’s Wharf. There are two buildings. We were in the … - 

$126

$126
Grand Hyatt San Francisco Union Square

Grand Hyatt San Francisco Union Square

345 Stockton St, San Francisco
4.5 out of 5.0
4.4 out of 5 (3,344 reviews)
Good Location Clean hotel with a great staff and a very good location. Union Square is a great place for shopping - 

$169

$169
Fairmont San Francisco

Fairmont San Francisco

950 Mason Street Atop Nob Hill, San Francisco
5.0 out of 5.0
4.5 out of 5 (3,843 reviews)
Great hotel in beautiful San Francisco. Only downside is that you have to walk up a big hill! - 

$199

$199
Handlery Union Square Hotel

Handlery Union Square Hotel

351 Geary St, San Francisco
4.0 out of 5.0
4.0 out of 5 (4,156 reviews)
SF Nostalgia We loved staying here, brought back many memories of old times living in SF! Hotel stay was great i … - 

$129

$129
Serrano Hotel

Serrano Hotel

405 Taylor St, San Francisco
4.5 out of 5.0
4.0 out of 5 (4,484 reviews)
Great boutique style hotel blocks from union squar I’ve been staying here for 12 years and now they are renovating the hotel after so long and it’s wo … - 

$138

$138
The Park Central San Francisco

The Park Central San Francisco

50 3rd St, San Francisco
4.5 out of 5.0
4.3 out of 5 (5,874 reviews)
Thanksgiving in the city Took the family to the city for a get away thanksgiving weekend. Very nice hotel but expect to pay … - 

$114

$114
Hotel Zephyr

Hotel Zephyr

250 Beach Street, San Francisco
4.0 out of 5.0
4.2 out of 5 (2,389 reviews)
Great location in Fisherman's wharf area Great Hotel, great location, when we visited, they were in the process of building their restaurant … - 

$161

$161
San Francisco Marriott Marquis

San Francisco Marriott Marquis

780 Mission Street, San Francisco
4.0 out of 5.0
4.3 out of 5 (3,792 reviews)
Nice comfortable hotel. No Jacuzzi though. Great experience and view. Didn't know I had to pay over $70 per night just for parking. Didn't lik … - 

$170

$170
Chancellor Hotel on Union Square

Chancellor Hotel on Union Square

433 Powell St, San Francisco
3.5 out of 5.0
4.3 out of 5 (3,563 reviews)
Amazing! Wonderful hotel. I can’t believe what a great find this was. Great view of the Christmas tree in un … - 

$107

$107
Omni San Francisco Hotel

Omni San Francisco Hotel

500 California St, San Francisco
5.0 out of 5.0
4.7 out of 5 (3,332 reviews)
Nice Hotel Centrally located in SFO Hotel is very nice, staff were very friendly and professional. I would recommend anyone stay at thi … - 

$166

$166
Argonaut Hotel - a Noble House Hotel

Argonaut Hotel - a Noble House Hotel

495 Jefferson St, San Francisco
5.0 out of 5.0
4.6 out of 5 (5,621 reviews)
Amazing location, nice staff, interesting nautical theme but not excessive. - 

$142

$142
Map

Recently booked San Rafael hotels

Embassy Suites by Hilton San Rafael Marin County
4.0 out of 5.0
Last booking: 2 hours ago
Travelodge in San Rafael
2.5 out of 5.0
Last booking: 8 hours ago
Four Points By Sheraton San Rafael
4.0 out of 5.0
Last booking: 20 hours ago
Marin Lodge
2.5 out of 5.0
Last booking: 25 hours ago
North Bay Inn
2.5 out of 5.0
Last booking: 27 hours ago
Extended Stay America San Rafael - Francisco Boulevard East
3.0 out of 5.0
Last booking: 27 hours ago
Villa Inn
2.5 out of 5.0
Last booking: 32 hours ago

Independent San Rafael Hotel Guide

Some globe-trotters choose hotels based on location, but others book by name. And thanks to Expedia you don’t have to pick. It is why we offer such an expansive range of Independent hotels in San Rafael, California. Known for well-appointed rooms and friendly, personalized service, each of the top Independent San Rafael hotels guarantees an unparalleled level of comfort and quality.

You’ll find best-in-class amenities like clean rooms and quiet atmospheres, and some San Rafael Independent locations may even offer extra little benefits and discounts for frequent travelers.