SFWHS participates in interscholastic athletics in the Bay Area Conference, the second largest conference in the North Coast Section (NCS) of the California Interscholastic Federation (CIF). All California school athletics, whether public or private, are under the jurisdiction of the CIF.
The Bay Area Conference consists of four leagues, the BCL, BCL-East, the BCL-Central, and the BCL-West. The BCL-Central includes Gateway, International, Leadership, Pescadero, San Domenico, SFWHS, and the Bay School. Schools in the West include Convent of the Sacred Heart, Stuart Hall, Lick-Wilmerding, Marin Academy, University, Urban, and Drew. Schools in the BCL are California School for the Deaf, Contra Costa Christian, Cornerstone Christian, Chinese Christian, Fremont Christian and Oakland Military Institute. Schools in the BCL-East are Athenian, Bentley, College Preparatory, Head-Royce, Redwood Christian, St. Elizabeth, and Valley Christian (Dublin).
SF Waldorf High School endorses the athletic principles of the California Interscholastic Federation, the North Coast Section, the Bay Area Conference, and the Bay Counties Leagues.