Boutique Hotels & Resorts in San Juan Island from NZ$268
Change your mindBook hotels with free cancellation
Be pickySearch almost a million properties worldwide
Check availability on San Juan Island Boutique Hotels
No exact matches found, but these alternatives could be just right
Recommended hotels in San Juan Island
9.8 out of 10, Exceptional, (247)
"How lovely and personable everything was.
The room was super nice and cozy.
Loved the breakfast. It was so well made.
And what a special experience to get to feed the alpacas and the goats! "
CECILIA
The price is NZ$299
includes taxes & fees
18 Jan - 19 Jan 2026
9.8 out of 10, Exceptional, (438)
"The Best Resort on the island! - Waterfront, quiet, clean, friendly, cozy, all the amenities you could ask for. The most relaxing location you've ever been to. Once you arrive, you'll never want to leave. I will be coming back soon! "
Brock
The price is NZ$392
includes taxes & fees
6 Jan - 7 Jan 2026
9.2 out of 10, Wonderful, (416)
"Nice clean and comfy rooms. Staff was really friendly and helpful. "
David
8.4 out of 10, Very good, (1000)
"Great room, great staff, love the hotel. This will be our go to for visits here! "
Nathaniel
The price is NZ$365
includes taxes & fees
14 Jan - 15 Jan 2026
9.4 out of 10, Exceptional, (281)
"Lovely cabin (Lizzie’s house), very dog friendly (they had a cupcake for him on arrival), and delicious breakfasts and cookies. Thanks for the relaxing stay!"
David
The price is NZ$268
includes taxes & fees
6 Jan - 7 Jan 2026
8.8 out of 10, Excellent, (362)
"The electronic check-in went smoothly and the location was great. Room was comfortable and the area was quiet. "
Bret
The price is NZ$276
includes taxes & fees
11 Jan - 12 Jan 2026
9.6 out of 10, Exceptional, (244)
"Beautiful location, nice room, and helpful staff. It was the perfect spot for a cozy wintertime island escape!"
Julie
The price is NZ$432
includes taxes & fees
14 Jan - 15 Jan 2026
8.8 out of 10, Excellent, (998)
"Great place clean room. Nice people. "
Jim
The price is NZ$400
includes taxes & fees
1 Jan - 2 Jan 2026
Lowest nightly price found within the past 24 hours based on a 1 night stay for 2 adults. Prices and availability subject to change. Additional terms may apply.
Top San Juan Island Hotel Reviews
Explore a world of travel with Expedia
- Hilton Hotels in San Juan Islands
- Stuart Island Hotels
- Lopez Island Hotels
- Eastsound Hotels
- Friday Harbor Hotels
- Roche Harbor Hotels
- Olga Hotels
- Anacortes Hotels
- Lummi Island Hotels
- Rosario Hotels
- Hotels near Stuart Island
- Orcas Hotels
- Blakely Island Hotels
- Hotels near San Juan Islands Sculpture Park
- Doe Bay Hotels
- Romantic Hotels in Ferndale
- Spa Hotels in Ferndale
- Luxury Hotels in Fairhaven
- Historic Hotels in San Juan Island
- Luxury Hotels in San Juan Island
- Family Hotels in San Juan Island
- Lgbt Welcoming Hotels in San Juan Island
- Luxury Hotels in Friday Harbor
- Beach Hotels in Mount Vernon
- Ski Hotels in Mount Vernon
- Pet Friendly Hotels in Mount Vernon
- Cheap Hotels in Northwest Washington
- Spa Hotels in Bellingham
- Cheap Hotels in Bellingham
- Adventure Sport Hotels in La Conner
- Beach Hotels in La Conner
- Hotels with Pool in Birch Bay
- Beach Hotels in San Juan Islands
- Luxury Hotels in San Juan Islands
- Luxury Hotels in Port Townsend
- Luxury Hotels in Orcas Island
- Romantic Hotels in Orcas Island
- Boutique Hotels in Orcas Island
- Cheap Hotels in Orcas Island
- Cottages in Roche Harbor
- Resort in Guemes Island
- Resort in Rosario
- Cabin Rentals in Stuart Island
- Cabin Rentals in Orcas Island
- Farmstay in Orcas Island
- Apartments in Orcas Island
- Caravan Parks in Orcas Island
- Condo Rentals in Orcas Island
- Cottages in Orcas
- Apartments in San Juan Islands
- Cabin Rentals in San Juan Islands
- Resort in San Juan Islands
- B&B in San Juan Islands
- Resort in San Juan Island
- Inns in San Juan Island
- Cabin Rentals in Lummi Island
- B&B in Friday Harbor
- Flights from Lopez Island
- Flights from Orcas Island
- Flights from Lummi Island
- Flights from San Juan Islands
- Flights from Redmond (RDM) to Anacortes (OTS)
- Flights from Kodiak (ADQ) to Lopez Island (LPS)
- Flights from Los Angeles (LAX) to Decatur Island (DTR)
- Flights from Chicago (ORD) to Decatur Island (DTR)
- Flights from Lopez Island
- Flights to Sucia Island
- Rent A Wreck Rental Cars in San Juan Island
- Nü Car Rentals Rental Cars in San Juan Island
- Keddy By Europcar Rental Cars in San Juan Island
- Rent A Wreck Rental Cars in San Juan Islands
- Keddy By Europcar Rental Cars in San Juan Islands
- National Car Rental Rental Cars in Friday Harbor Sea Plane Base
- Car hire in Avis 1333 N Highland Ave
- Rental cars Friday Harbor airport
- Car hire Anacortes
- Rental cars Lopez Island airport