Boutique hotel vacation rentals in San Juan County

Find and book unique boutique hotel rentals on Airbnb

Top-rated boutique hotel rentals in San Juan County

Guests agree: these boutique hotel rentals are highly rated for location, cleanliness, and more.

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Guest favorite

Hotel room in Friday Harbor

5 out of 5 average rating, 7 reviews

Regal Royale room at Juniper Lane

A unique, authentic, inspired, inn, on San Juan since 2004! At Juniper Lane, we take great pride in offering comfortable and sparkly rooms, quality linens, a relatively economical rate, and a rural setting with the town of Friday Harbor close by (1.3 miles from the ferry landing). The Innkeeper, Juniper, is a multi-generational islander, that spent her 20's traveling the world scoping lodging intel, and built the inn with a small group of talented craftspeople, she is so lucky to call friends!

Guest favorite

Hotel room in Friday Harbor

5 out of 5 average rating, 75 reviews

Private guesthouse w/ hot tub & breathtaking views

Your private guesthouse awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian-style, boutique inn situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your separate and private guesthouse with breathtaking views, modern amenities, and miles of trails, gardens, and natural beauty to explore. Cedar hot tub in the deck overlooking the Salish Sea, outdoor shower, and pet friendly for friendly pets! KING bedroom + QUEEN loft + DOUBLE sleeper sofa + bthrm.

Superhost

Hotel room in Friday Harbor

4.94 out of 5 average rating, 17 reviews

Private suite w/ exceptional views & soaking tub

Your exceptional private suite awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian farm-style boutique inn, situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your luxurious suite atop the architectural award-winning Inn, complete with large bathroom and soaking tub, separate living area with kitchenette, modern amenities, and miles of trails, gardens, and natural beauty to explore. KING bedroom + DOUBLE sleeper sofa + Living area + bathroom.

Guest favorite

Hotel room in Friday Harbor

4.99 out of 5 average rating, 95 reviews

Private guesthouse immersed in nature

Your private guesthouse awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian-style, boutique inn situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your separate and private guesthouse with breathtaking views, modern amenities, and miles of trails, gardens, and natural beauty to explore. Private deck & floor-to-ceiling windows with a cozy & intimate woodsy view. Wheelchair accessible. KING bedroom + QUEEN loft + DOUBLE sleeper sofa + bathroom.

Guest favorite

Hotel room in Friday Harbor

4.98 out of 5 average rating, 57 reviews

Private guesthouse w/ deck & breathtaking views

Your private guesthouse awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian-style, boutique inn situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your separate and private guesthouse with breathtaking views, modern amenities, and miles of trails, gardens, and natural beauty to explore. Private deck overlooking the Salish Sea, outdoor shower, and pet-friendly for friendly pets! KING bedroom + QUEEN loft + DOUBLE sleeper sofa + bathroom.

Guest favorite

Hotel room in Friday Harbor

5 out of 5 average rating, 5 reviews

Pine room at Juniper Lane 2 beds

Our Pine room is perfect for two people traveling together that want their own beds and a little more privacy, with the separate bathroom, located just a few feet across from your door. The room has a queen bed as well as a twin bunk (the twin beds are built into the wall with beams and are solid and independent of each other). The Pine room has a lovely view of the valley, beautifully handcrafted trim details made of rare, high altitude old-growth cedar, and knotty pine wainscoting.

Guest favorite

Hotel room in Friday Harbor

4.98 out of 5 average rating, 55 reviews

Private guesthouse surrounded by majestic firs

Your private guesthouse awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian-style, boutique inn situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your separate and private guesthouse with breathtaking views, modern amenities, and miles of trails, gardens, and natural beauty to explore. Light & bright, private deck, floor-to-ceiling windows & an intimate woodsy view. KING bedroom + QUEEN loft + DOUBLE sleeper sofa + bathroom.

Hotel room in Friday Harbor

4.6 out of 5 average rating, 85 reviews

Wayfarers Guest House. Room #4, the Forecastle

Thank you for finding the Wayfarers Rest, providing comfortable and convenient lodging for active travelers since 1999. Room 4 is a private room that can sleep only 2, all linens provided. The common areas you will share with other guests (fully equipped kitchen, dining, living room and bathrooms) Wayfarers Rest is located just 4 blocks from the ferry terminal and two blocks from main St., easy walking. Free Wi-Fi, parking & chicken eggs.

Guest favorite

Hotel room in Lopez Island

4.88 out of 5 average rating, 50 reviews

~VintageLuxury~ SoakingTub Fireplace King Bed WiFi

✔ No Cleaning Fees ✔ Super Fast WIFI ✔ Fireplace ✔ Full Bathroom w. Soaking Tub ✔ In Room Coffee + Decaf & Tea ✔ Leather couch + King Sleigh Bed ✔ Access to All Common Spaces at Edenwild Boutique Hotel ✔ 24/7 Staff that are here when you need them and never when you don't :) ✔ TV Free Property- Bring your Tablet for Movies ✔ Free Parking Our commitment to you has made us TripAdvisors #1 Hotel in the San Juan Islands.

Superhost

Hotel room in Friday Harbor

5 out of 5 average rating, 3 reviews

Unique private suite w/ forest & meadow views

Your unique 700+ sqft suite awaits at ~ at Saltwater Farm ~ a modern, Scandinavian farm-style abode, situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your large private suite above our stunning new barn with kitchen, modern amenities, DSL WiFi internet, and miles of trails, gardens, and natural beauty to explore. KING bedroom + 2 DOUBLE sleeper sofa loft + TWIN bedroom + bathroom

Guest favorite

Hotel room in Friday Harbor

4.98 out of 5 average rating, 40 reviews

Cedar & Mandala two bedroom suite at Juniper Lane

Juniper Lane Guest House, a hip and unique boutique Inn on San Juan Island. This unique Friday Harbor accommodations is a custom crafted bold mosaic of exotic woods, tile, art, and color. Nestled on the edge of Friday Harbor overlooking Beaverton Valley it has a rural feel yet is still close to town. This Boutique Inn offers a variety of accommodations that are “brilliant and affordable” for everyone.

Guest favorite