Transit services around Port Townsend began in 1915 with the debut of passenger "jitney" buses operated by private companies.

The Stevens Stage Line, successor to the original jitney in Port Townsend, was contracted by the Clallam-Jefferson Community Action Council in 1979 to operate a pilot transit route using funds from the Urban Mass Transportation Administration.

[1][2] Jefferson Transit expanded its operations to include connections to Forks on the west side of the Olympic Peninsula in 1995.

[2] Following the boarding of a private bus near Port Townsend by U.S. Border Patrol agents, Jefferson Transit allowed the American Civil Liberties Union to post English and Spanish signs in buses with information on civil rights in early 2009.

[6] Jefferson Transit became a fare-free system on January 2, 2024, when it stopped collecting fares on all routes.