Boyer was educated at Brigham Young University and at the University of Wisconsin, where he gained his PhD in 1943. He then taught at the universities of Wisconsin, Stanford, and Minnesota before being appointed professor of biochemistry at UCLA in 1963.

A basic problem in biochemistry is explaining how the energy-rich compound adenosine triphosphate (ATP) is used to fuel cellular activities and how, once used, it is recovered. Work by Peter Michell had identified a difference in hydrogen-ion concentration across the cell's mitochondrial membrane. Further investigation revealed in broad outline that energy was derived from adenosine diphosphate (ADP) in a reaction catalysed by the enzyme ATP synthase. Energy is released when one of the phosphate bonds of ATP breaks and becomes available for such tasks as muscle contraction. ADP is then converted back to ATP through the action of ATP synthase.

Boyer, from the 1970s onwards, began to throw more light on this process. It was found that ATP synthase came in three parts: a wheel-like assembly in the mitochondrial membrane, an attached rod, and a cylinder joined to the rod's other end located within the mitochondria. Boyer proposed that the hydrogen ions spin the wheel as they pass through the mitochondrial membrane, turning the rod and cylinder at the same time. The rotation of the cylinder attracts ADP and phosphate groups in the first step to synthesizing ATP.

Further light has been thrown on the reaction by John Walker and Jens Skou, with whom Boyer shared the 1997 Nobel Prize for chemistry.