A recipient of the Save America's Treasures Award by the National Trust for Historic Preservation, it is recognized as one of the oldest Japanese-style residential gardens in the Western Hemisphere.

[1] In 1915, two San Francisco arts patrons, Oliver and Isabel Stine, intending to build a summer retreat, purchased the 18-acre (7.3 ha) site on which Hakone now stands.

Inspired by the Panama–Pacific International Exposition and her subsequent 1916 trip to Japan, Isabel Stine modeled the gardens upon (and named them after) Fuji-Hakone-Izu National Park.

[2]: 25  In 1923, the west coast premiere of Puccini's Madama Butterfly was held in the gardens; Isabel Stine was a co-founder and patron of the producing company, the San Francisco Opera.

[3][4] In 1961, Joseph and Clara Gresham, their son Eldon and his wife Deon, and four Chinese American couples (George and Marie Hall, Johnny Kan and Helen Kan, Dan and June Lee, Col. John C. Young and Mary Lee Young) purchased the estate.

The original main gardens, ponds, waterfalls, and walkways were restored, and a new series of trails on the southwest hillside were constructed.

[3] The historic on-site structures were constructed using traditional Japanese designs and carpentry, based on 16th and 17th century residences favored by the samurai warrior class.