Search Cottages in San Juan Island

    calendar shield illustration

    Change your mind

    Book hotels with free cancellation
    deals illustration

    Treat yourself

    Sign in to save 10% or more on thousands of hotels
    Sign in
    bed illustration

    Be picky

    Search almost a million properties worldwide

Check prices for these dates

Next weekend
Aug 22 - Aug 24
In two weeks
Aug 29 - Aug 31
In one month
Sep 12 - Sep 14
In two months
Oct 10 - Oct 12

Cottages in San Juan Island

Swan Lake Cottage by Avantstay Views + Firepit
House (2 Bedrooms) | Interior

Swan Lake Cottage by Avantstay Views + Firepit

3.0 star property
Swan Lake Cottage by Avantstay Views + Firepit
Penn Cove Overlook by Avantstay Cabin w/ Views
House (1 Bedroom) | Interior

Penn Cove Overlook by Avantstay Cabin w/ Views

3.0 star property
10.0 out of 10, Exceptional, (2)
"Really loved how private and quiet it was. It was so cute and comfortable. Would love to go back and stay longer."
Penn Cove Overlook by Avantstay Cabin w/ Views
Oak Harbor Hideaway - 5 Mi to Deception Pass!
Outdoor dining

Oak Harbor Hideaway - 5 Mi to Deception Pass!

3.0 star property
Oak Harbor Hideaway - 5 Mi to Deception Pass!
Bayfront Home - Take Ferry to the San Juan Islands
House (3 Bedrooms) | Interior

Bayfront Home - Take Ferry to the San Juan Islands

3.0 star property
10.0 out of 10, Exceptional, (1)
Bayfront Home - Take Ferry to the San Juan Islands
@ Marbella Lane - Seas the Bay Sanctuary
House (3 Bedrooms) | Beach/ocean view

@ Marbella Lane - Seas the Bay Sanctuary

3.0 star property
The price is NT$6,119
NT$14,445 total
includes taxes & fees
Sep 2 - Sep 3
@ Marbella Lane - Seas the Bay Sanctuary
@ Marbella Lane Wave HS W/ev Charger, Oceanfront!
Front of property - evening/night

@ Marbella Lane Wave HS W/ev Charger, Oceanfront!

3.0 star property
The price is NT$8,159
NT$16,705 total
includes taxes & fees
Sep 2 - Sep 3
@ Marbella Lane Wave HS W/ev Charger, Oceanfront!
Stunning Home in Coupeville w/ Deck + Beach Access
House (2 Bedrooms) | Private kitchen | Microwave, oven, stovetop, dishwasher

Stunning Home in Coupeville w/ Deck + Beach Access

3.0 star property
10.0 out of 10, Exceptional, (3)
"Very close to the shore, but easier to access from nearby Park. Loved the home and location. Everything we needed was available to use. Can't wait to stay again!"
Stunning Home in Coupeville w/ Deck + Beach Access
West Beach Wonderland by Avantstay Waterfront
House (2 Bedrooms) | Interior

West Beach Wonderland by Avantstay Waterfront

3.0 star property
West Beach Wonderland by Avantstay Waterfront
Lopez Island Hideaway w/ Coastal Views + Deck!
House (4 Bedrooms) | Interior

Lopez Island Hideaway w/ Coastal Views + Deck!

3.0 star property
10.0 out of 10, Exceptional, (1)
"Very spacious house and great yard. Great location close to Lopez village. Will stay here again when visiting Lopez."
Lopez Island Hideaway w/ Coastal Views + Deck!
Anacortes Paradise Vacation Rental w/ Water Views!
House (2 Bedrooms) | Interior

Anacortes Paradise Vacation Rental w/ Water Views!

3.0 star property
Anacortes Paradise Vacation Rental w/ Water Views!
West Beach Lookout by Avantstay Walk to Beach
Interior

West Beach Lookout by Avantstay Walk to Beach

3.0 star property
6.0 out of 10, (1)
"Run by a management company. Pet fee not listed and after we paid they told us it was more for our dog for 3 days. Asked for a refund told no we had to lose half after booking if we cancel.. ya right. Ended up coughing up additional money. Frankly kinda crappy. They now have the pet fee as super high per day on site which I'm sure is also an error since they told us way lower per day. I won't be booking an house again with the site. Once they have your money, your out of luck if extra...
West Beach Lookout by Avantstay Walk to Beach
Anacortes Home w/ Views of Puget Sound
House (3 Bedrooms) | Interior

Anacortes Home w/ Views of Puget Sound

3.0 star property
6.0 out of 10, (1)
"The house is super clean and well stocked. Great view, nice neighborhood, close to ferry and to town and state park. But, the host is not flexible and cooperative. And the bed in the master bedroom is the worst. Keeps creaking with every turn and the mattress is so hard, you may as well be sleeping on a camping mat. Keep in mind, there no ceiling fans or AC and it was HOT in August and very uncomfortable to sleep at night. "
Anacortes Home w/ Views of Puget Sound
Seacliff Haven Waterfront Luxury, Stunning Views, Hot Tub & Game Room
House (5 Bedrooms) | Interior

Seacliff Haven Waterfront Luxury, Stunning Views, Hot Tub & Game Room

3.0 star property
Seacliff Haven Waterfront Luxury, Stunning Views, Hot Tub & Game Room
Custom Guemes Home w/ Spectacular Water Views!
House (3 Bedrooms) | Private kitchen | Microwave, oven, stovetop, dishwasher

Custom Guemes Home w/ Spectacular Water Views!

3.0 star property
Custom Guemes Home w/ Spectacular Water Views!
Similk Bay Retreat With Deck, Fire Pit + Hot Tub!
House (4 Bedrooms) | Interior

Similk Bay Retreat With Deck, Fire Pit + Hot Tub!

3.0 star property
Similk Bay Retreat With Deck, Fire Pit + Hot Tub!
Coastal Haven w/ Hot Tub & San Juan Island Views
House (1 Bedroom) | Private kitchen | Microwave, oven, stovetop, blender

Coastal Haven w/ Hot Tub & San Juan Island Views

3.0 star property
Coastal Haven w/ Hot Tub & San Juan Island Views
Lodge Trails, Hot Tub, Walk to Cornet Bay
House (4 Bedrooms) | Front of property

Lodge Trails, Hot Tub, Walk to Cornet Bay

3.0 star property
Lodge Trails, Hot Tub, Walk to Cornet Bay
2 Blocks to Puget Sound Beach: Lummi Island Home
House (3 Bedrooms) | Interior

2 Blocks to Puget Sound Beach: Lummi Island Home

3.0 star property
2 Blocks to Puget Sound Beach: Lummi Island Home
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.
Save an average of 15% on thousands of hotels when you're signed in
Sign in
Sign up, it's free

Top San Juan Island Hotel Reviews

Earthbox Inn & Spa

Earthbox Inn & Spa

10/10 Excellent
"Great place! Close to everything and quiet!"
Jessica 2-night trip
Posted 15 hours ago
Earthbox Inn & Spa

Frequently asked questions

Why book your cottage in San Juan Island with Expedia?
Expedia has some excellent cottages in San Juan Island, so get ready for a memorable vacay close to nature. If you have a set budget, select how much you're willing to spend and the star rating of your property. Or, use our filters to search for cottages with a hot tub or free WiFi. We'll help you find the perfect place whatever your plans or style of travel.
How can I find cheap cottages in San Juan Island?
Expedia can help you locate cheap cottages in San Juan Island. To book your dream stay in a few clicks, simply use the filter tool to refine your search by star rating, budget and amenities.