DeGraffenreid served as a Senior professional staff member of the Senate Select Committee on Intelligence (1977-81). He wasSenior Director of Intelligence Programs, National Security Council (1981-1987). He served as Deputy Under Secretary of Defense for Policy Support, Department of Defense (2001-2004).
According to journalist Seymour Hersh, deGraffenreid left the Pentagon after Stephen Cambone won control of special access intelligence programmes that deGraffenreid had been responsible for monitoring.
Degraffenreid was Deputy National Counterintelligence Executive (2004-2005).