The museum originally opened in 1895 as an outgrowth of the California Midwinter International Exposition of 1894 (a fair modelled on the Chicago World's Columbian Exposition of the previous year). The building was originally decorated with cast-concrete ornaments on the facade. The ornaments were removed in 1949 as they began to fall and had become a hazard. The 1989 Loma Prieta Earthquake severely damaged the building.
Architects Jacques Herzog and Pierre de Meuron designed the newly rebuilt structure, which reopened on October 15, 2005. Copper plating, which will change colors through exposure to the elements, surrounds the present building. A 144 ft. observation tower allows visitors to see much of Golden Gate Park's Music Concourse.
As part of the agreement that created the Fine Arts Museums of San Francisco in 1972, the de Young's collection of European art was sent to the Legion of Honor. In compensation, the de Young received the right to display the bulk of the organization's anthropological holdings. These include significant pre-Hispanic works from Teotihuacan and Peru, as well as indigenous tribal art from sub-Saharan Africa.