Mr. Oberndorf partnered with the late John Walton in the early 1990s to form what today is known as the American Federation for Children where he serves as Chairman. Mr. Oberndorf, and his wife, Susan, have been active philanthropists since the mid-1980s. Together they serve as co-presidents of the Oberndorf Foundation.

The focus of the Foundation is on K–12 education, mental health initiatives, and the environment. He is a life trustee of the University of California San Francisco where he chairs the Neuroscience Academy. Mrs. Oberndorf serves on the board of the Environmental Defense Fund and numerous committees at Stanford University.