Born in Santa Barbara, California, he studied at College of Puget Sound for a year before transferring to Harvard University, where he earned a bachelor's degree in 1930. Encouraged by Samuel Eliot Morison to change his postgraduate focus to history, he received master's and doctoral degrees in that field during the 1930s.
- Sam Adams, Pioneer in Propaganda. Stanford University Press, 1936. ISBN 9780804700245.
- Crisis in Freedom: The Alien and Sedition Acts. Little, Brown, 1951. ISBN 978-0316572330.
- Origins of the American Revolution: With a New Introd, and a Bibliography. Stanford University Press, 1959. ISBN 9780804705936.
- The Federalist Era 1789-1801. Harper and Brothers, 1960. ISBN 978-1577660316.
- The Wolf by the Ears: Thomas Jefferson and Slavery. Published with the Thomas Jefferson Memorial Foundation, University Press of Virginia, 1991. ISBN 9780813913650.
- The Wolf by the Ears. Indiana Museum of History. .
- Crisis in Freedom: The Alien and Sedition Acts. The Pennsylvania Magazine of History and Biography. 
- The Federalist Era. The American Historical Review. 
- "MEMORIAL RESOLUTION JOHN CHESTER MILLER" (PDF). Stanford University. Archived from the original (PDF) on 2013-11-12. Retrieved 2013-11-12.
- "John C. Miller, 83; Writer and Professor Of American History". New York Times. Retrieved 2013-11-12.