Search San Juan Island Cottage Rentals

    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
25 Jul - 27 Jul
In two weeks
1 Aug - 3 Aug
In one month
15 Aug - 17 Aug
In two months
12 Sept - 14 Sept

Featured Cottages in San Juan Island

Penn Cove Overlook by Avantstay Cabin w/ Views
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
Swan Lake Cottage by Avantstay Views + Firepit
Interior

Swan Lake Cottage by Avantstay Views + Firepit

3.0 star property
Swan Lake Cottage by Avantstay Views + Firepit
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!
Stunning Home in Coupeville w/ Deck + Beach Access
Private kitchen

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
Lopez Island Hideaway w/ Coastal Views + Deck!
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!
Interior

Anacortes Paradise Vacation Rental w/ Water Views!

3.0 star property
Anacortes Paradise Vacation Rental w/ Water Views!
Bayfront Home - Take Ferry to the San Juan Islands
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
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
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
@ 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 S$946
includes taxes & fees
20 Jul - 21 Jul
@ Marbella Lane Wave HS W/ev Charger, Oceanfront!
Custom Guemes Home w/ Spectacular Water Views!
Private kitchen

Custom Guemes Home w/ Spectacular Water Views!

3.0 star property
Custom Guemes Home w/ Spectacular Water Views!
Coastal Haven w/ Hot Tub & San Juan Island Views
Private kitchen

Coastal Haven w/ Hot Tub & San Juan Island Views

3.0 star property
Coastal Haven w/ Hot Tub & San Juan Island Views
Similk Bay Retreat With Deck, Fire Pit + Hot Tub!
Interior

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

3.0 star property
Similk Bay Retreat With Deck, Fire Pit + Hot Tub!
West Beach Wonderland by Avantstay Waterfront
Interior

West Beach Wonderland by Avantstay Waterfront

3.0 star property
West Beach Wonderland by Avantstay Waterfront
@ Marbella Lane - Seas the Bay Sanctuary
Beach/ocean view

@ Marbella Lane - Seas the Bay Sanctuary

3.0 star property
The price is S$829
includes taxes & fees
12 Aug - 13 Aug
@ Marbella Lane - Seas the Bay Sanctuary
Seacliff Haven Waterfront Luxury, Stunning Views, Hot Tub & Game Room
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
2 Blocks to Puget Sound Beach: Lummi Island Home
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

Anacortes Ship Harbor Inn

Anacortes Ship Harbor Inn

10/10 Excellent
"Beautiful property within sight of the ferry dock. Exceptional views, nice sitting areas, working electric car charger, convenient parking, well-kept grounds. Our room had a hot tub with a view of the water. We would definitely stay again!"
David 1-night trip
Posted 2 days ago
Anacortes Ship Harbor Inn

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 holiday 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.