The area along the Sammamish River, including modern-day Woodinville, is the historic territory of the indigenous Sammamish people. Other Coast Salish peoples also occupied and used the lands in the area, including a Duwamish subgroup known as the “willow people”.

In 1871, Ira Woodin and his wife Susan moved from Seattle and traveled up the Sammamish River where they built a cabin. They planned to log timber and farm cattle. A town gradually developed around them. Their cabin served as its first school and post office, with Susan Woodin appointed as postmaster. Woodin and his son-in-law Thomas Sanders set up the first general store.

Like other nearby towns, Woodinville began as a logging community and became a farming center in the early decades of the 20th century. After World War II, it developed as a suburb of Seattle. In 1969, rock bands including Led Zeppelin and The Guess Who performed at the Seattle Pop Festival at Woodinville’s Gold Creek Park.

The community sought either incorporation as a city or annexation by neighboring Bothell in the 1970s to improve services. A later attempt by Bothell to annex portions of Woodinville in 1985 was halted but inspired an incorporation campaign. The residents of Woodinville voted for incorporation on May 19, 1992, the third attempt at becoming a city; a previous attempt had been rejected by a margin of 14 votes. Woodinville was officially incorporated on March 27, 1993.

In the late 1990s, Woodinville attempted to annex the adjacent community of Grace in Snohomish County. The county’s government and the State Boundary Review Board rejected the proposal, citing the loss of tax revenue and legal issues with providing policing due to Woodinville’s contracts with the King County Sheriff’s Office. The area was also considered for a branch campus of the University of Washington that was ultimately built in Bothell.