Architectural firm A. W. Longfellow broke ground on the present HMANE site on September 27, 1900.

Construction was completed in spring of 1902, and the public portions of the museum were opened on February 5, 1903.

[2]: 22 The museum's facilities were repurposed during World War II, and it was closed to the public from August 1942 through April 1946.

On October 14, 1970, a bomb was detonated on the third floor of the museum amid protests on campus against the Vietnam War.

In April 2020, Peter Der Manuelian, director of the museum, announced changing its name to the Harvard Museum of the Ancient Near East (HMANE), explaining that "The change is not a reaction to any particular event, but rather our attempt to reflect our core mission in clearer terms.