The community got its start in 1897 when miners discovered gold on Willow Creek. Ships and boats brought supplies and equipment up Cook Inlet, landing at Knik or Tyonek. From Knik, a 26-mile summer trail went northwesterly. The trail along Willow Creek heading east became Hatcher Pass Road, currently an adventurous scenic road used during the summer tour season.
During World War II, a radar warning station and airfield were built near the railroad tracks; a post office was established in 1948.
By 1954, Willow Creek was Alaska's largest gold mining district, with a total production approaching 18 million dollars.
Around 1970, before construction of the Parks Highway, Willow had a population of 78 until land disposals, homestead subdivisions, and completion of the George Parks Highway in 1972 fueled growth in the area.
In 1976, Alaskans elected to move the state capital from Juneau to Willow in an effort to improve access for Alaskans while keeping the capital out of Anchorage, the largest city. Landscape architect M. Paul Friedberg created a master plan for the city as part of one such proposal. This fueled interest and land speculation in the area. However, funding to enable the capital move was defeated in the November 1982 election. As a result, Juneau remains the state capital.
More than half of the 1,500 cabins around Willow are for seasonal-use. Nearly all of the occupied homes in Willow are fully plumbed, using individual on-site water wells, septic tanks and drain fields.