- San Juan County (Spanish: Condado de San Juan) is a county located in the Salish Sea in the far northwestern corner of the U.S. state of Washington. As of the 2020 census, its population was 17,788. The county seat and only incorporated city is Friday Harbor, located on San Juan Island. The county was formed on October 31, 1873, from Whatcom County and is named for the San Juan Islands, which are in turn named for Juan Vicente de Güemes, 2nd Count of Revillagigedo, the Viceroy of New Spain.