Bakker was born in Bergen County, New Jersey. He attributes his interest in dinosaurs to his reading an article in the September 7, 1953 issue of Life magazine. He graduated from Ridgewood High School in 1963.
At Yale University, Bakker studied under John Ostrom, an early proponent of the new view of dinosaurs, and later gained a PhD at Harvard. He began by teaching anatomy at Johns Hopkins University in Baltimore, Maryland and Earth and Space Sciences, where future artist Gregory S. Paul worked and collaborated informally under his guidance. Most of his field work has been done in Wyoming, especially at Como Bluff, but he has ranged as far as Mongolia and South Africa in pursuit of dinosaur habitats.