Founded in 1901 under the patronage of Phoebe Apperson Hearst, the original goal of the museum was to support systematic collecting efforts by archaeologists and ethnologists in order to support a department of anthropology at the University of California.

The museum was originally located in San Francisco from 1903 (open to the public as of 1911) until 1931, when it moved to the campus of the University of California, Berkeley.

In 1991, the museum's name was changed to recognize the essential role of Phoebe Apperson Hearst as founder and patron.

These include the museum's first director Frederic Ward Putnam, the anthropologists Alfred L. Kroeber, Robert Lowie, and William Bascom, paleoanthropologists Francis Clark Howell and Tim D. White, Egyptologists Klaus Baer and Cathleen Keller, and archaeologists Max Uhle, George Reisner, John Howland Rowe, J. Desmond Clark, David Stronach, Crawford Hallock Greenewalt Jr. and Patrick Vinton Kirch.

The museum houses an estimated 3 million objects plus extensive documentation that includes fieldnotes, photographs, and sound and film recordings.