Born in Atlanta to a Presbyterian family of Scotch-Irish American and English descent, Pierce was a descendant of Thomas H. Watts, the Governor of Alabama and Attorney General of the Confederate States of America during the American Civil War. Pierce was academically successful, graduating from high school in 1952. He received a bachelor's degree in physics from Rice University in 1955, earned a doctorate from University of Colorado at Boulder in 1962, and became an assistant professor of physics at the Oregon State University in that year. In 1965 he left his tenure at Oregon State University and became a senior researcher for the aerospace manufacturer Pratt & Whitney in Connecticut. In 1966, Pierce moved to the Washington, D.C. area and became an associate of George Lincoln Rockwell, founder of the American Nazi Party, who was assassinated in 1967. Pierce became co-leader of the National Youth Alliance, which split in 1974, with Pierce founding the National Alliance.