During the period from 1804 to 1830 when the cultural aspects of townspeople of Edo began to thrive, Sahara Kiku-u, a wealthy dealer in antiques, established a garden for enjoying flowers in bloom with the help of other aficionados of the arts. One theory has it that the name "Hyakkaen" was chosen to mean "a garden with a hundred flowers that bloom throughout the four seasons." At the time when the garden first opened, its main feature was 360 ume trees. In later years, many different blooming flowers and plants mentioned in classic Chinese and Japanese works of literature and poetry were collected, enabling visitors to enjoy blooming flowers throughout the year. The garden is the only surviving flower garden from the Edo Period.


In 1938, in order to preserve the garden for posterity, the owner gave the garden to the City of Tokyo and it was officially opened to the public as a pay-to-view garden in 1939. In 1978, it was designated by the national government as a famous site of historical significance under the terms of the Cultural Assets Preservation Law.