San Juan Island Fire and Rescue is governed by San Juan County Fire District 3. The state of Washington chartered San Juan Island Fire Department in May of 1959.

In Washington, special purpose districts are limited purpose local governments separate from a city, town, or county government. Generally, they perform limited functions including fire protection, that are not otherwise available from city or county governments.

San Juan County Fire District 3 has an elected, three member board of commissioners. Most special purpose districts in Washington, including San Juan County District 3, derive revenues from real property assessments and are called taxing districts. 

Fire District #3 operates as directed by applicable laws and regulations set by the Revised Code of Washington (RCW) and the Washington Administrative Code (WAC).

The RCW is the compilation of all permanent laws now in force. It is a collection of Session Laws (enacted by the Legislature, and signed by the Governor, or enacted via the initiative process). The WAC includes the regulations of executive branch agencies issued by authority of statutes. Like legislation and the Constitution, regulations are a source of primary law in Washington State. The WAC codifies the regulations and arranges them by subject or agency.