Duffy has served as a Trustee, Chair of the Board, President of the Board, Director and Advisory Board member of some two dozen organizations nationally and locally in the Bay Area. These include the Boards of Directors of The Bulletin of the Atomic Scientists in Chicago and Computer Professionals for Social Responsibility in Palo Alto, California. She served as Board President of the Guadalupe River Park Conservancy, and served on the Board of Directors of Los Gatos Community Hospital, now El Camino Hospital. She has been a Trustee of Occidental College in Los Angeles since 2006, and is Vice Chair of its Executive Committee. She has chaired the Board's Academic Affairs Committee and co-chaired the Board's Student Life and Enrollment Management Committee. She served as a Trustee and on the Executive Committee of Dominican University of California, in San Rafael, California.