In 1915, inspired by both a lifelong interest in Japanese Culture and their travels throughout Japan, San Francisco cultural leaders Oliver and Isabel Stine purchased 18 acres of Saratoga hillside to build a summer retreat for family and friends. Stimulated by displays at the 1915 Pan-Pacific Exhibition, Stine traveled to Japan to gather ideas and when she returned home named her retreat after one of her favorite places in Japan, Fuji-Hakone National Park.

In 1918, she retained architect Tsunematsu Shintani (1877-1921) a native of Wakayama prefecture, to design the Upper "Moon Viewing" House and landscape gardener Naoharu Aihara (1870-1941), born to a family of Imperial gardeners in Koyobashi, Tokyo, to design the gardens.

The garden began on a logged out hillside with a dramatic view of the "Valley of the Heart's Delight", what Silicon Valley was then known as. During Japan's late Edo Period (early 19th century) hillside sansos, or country villas, were popular throughout Japan where the pond is set on the slope from which a waterfall can drop into the lake below. All the classic elements of a hill and pond garden can be found at Hakone where there is a master stone, a worshipping stone, guest Isle, meandering pathways with centuries old lanterns, and residential style architecture popular with samurai. The dramatic elevation change from the lower gardens to the Upper House (aligned for moon-viewing) is an ideal setting. The Upper House (built in 1917) includes a study space, a tokonoma or alcove, and a sliding door shelf. The architecture was developed by the tea masters and is characterized by lightness of design and use of natural materials, and minimal ornamentation; similar to the imperial villas in Kyoto where the tea houses are placed throughout the elaborate pond garden.

The Lower House was built in 1922 and became the caretaker's house in 1927. It features quality redwood craftsmanship, unpainted wood siding and beautiful Japanese-style architecture. Stine spent $100,000 (a considerable sum for that time) during the course of Hakone's construction from 1917 to 1929. She retained the finest Japanese builders and garden designers available. The pride of craftsmen trained during the Meiji era can be seen in their work.

In 1932, ownership passed to prominent East bay financier Major C.L. Tilden. He added the Mon, or main gate, to the Gardens. In 1961 Hakone was purchased by a partnership that included the families of Joseph and Eldon Gresham of Saratoga and three prominent families in San Francisco headed by George Hall, John Young, and John Kan and another prominent family from Palo Alto led by Dan Lee.

This group restored the neglected, overgrown gardens to their beautiful splendor. The families and their friends enjoyed Hakone as a private retreat. Hakone was well taken care of by the partnership, especially by the Chinese American families who had a special reverence for the gardens. In 1966 the partners decided to sell a beautifully restored Hakone to the City of Saratoga for all to enjoy. The City purchased Hakone at a price of $145,000. The City then hired Tanso Ishihara, a Kyoto trained Japanese Garden Specialist, who enhanced the gardens' classical Japanese design.

The camellia hillside and high trails were constructed at that time, the ponds and waterfalls were repaired, and stone pathways were repaired and pea gravel added. Gradually Ishihara pruned and restored the beauty of the original garden. Ishihara began consulting with the renowned Japanese architect Kiyoshi Yasui, a 14th generation architect to the Imperial Household who restored the famed Katsura Rikyu, and together they developed a master plan for expanding onto the surrounding 18-acre site.

While visiting Japan in 1980, Ishihara died in a tragic accident and friends from Japan and the United States joined forces to fulfill his dream for Hakone. Led by Yasui, they formed the Japan Bamboo Society and the Sister City program with Yasui's hometown of Muko and Saratoga.

In the intervening 23 years, many of the dreams which Ishihara and Yasui envisioned in the 1970s have been implemented. This includes the Bamboo Park, built in 1987, the Cultural Exchange Center built in 1990, and the tea plantation begun in 1995. Hakone continues to grow gracefully and harmoniously incorporates all the historic areas within the gardens.

Succeeding Ishihara was his student, Jack Tomlinson who studied in Kyoto and was appointed Japanese Garden Specialist. With Ishihara's wife, Tomlinson has worked to maintain the beauty and authenticity of Hakone Gardens.

In 1984, the Hakone Foundation was formed to preserve, enhance and maintain Hakone for future generations. In 2000, the Hakone Foundation signed an exclusive 55-year lease with the City of Saratoga to carry out this mission.