Stonesifer is a founding board member of the Academy of Interactive Arts and Sciences. She served on the board of The GAVI Fund, which helps to provide vaccines to developing countries. Stonesifer has also served on the U.S. delegation to the United Nations General Assembly Special Session on AIDS. She is a founding co-chair of the CITIES board, which promotes expanding the use of technology in Seattle's community colleges. Stonesifer donates both time and resources to a number of other regional nonprofit organizations; serves on the boards of the National Museum of African American History and Culture, Center for Global Development, and the Broad Institute; is a member of the Circle of Allies and Champions for the National Council of Young Leaders, the advisory board for America Achieves, and the executive committee of RaiseDC; and is a Hope Street Group advisor. Stonesifer served as a member of the U.S. delegation to the Joint United Nations Programme on HIV/AIDS and is a member of the American Academy of Arts and Sciences and the Council on Foreign Relations. She is also on the corporate board of Amazon.com. In 2012 she completed her term as chairman of the Smithsonian Institution Board of Regents.