Boyer was born in Pittsburgh, Pennsylvania, and educated at St. Vincent College, Latrobe, and the University of Pittsburgh where he obtained his PhD in 1963. He joined the faculty of the University of California, San Francisco, shortly afterward in 1966 and served as professor of biochemistry from 1976 to 1991.

Much of Boyer's work has been concerned with developing some of the basic techniques of recombinant DNA, known more popularly as genetic engineering. Thus in 1973 he succeeded with Robert Helling, and independently of the work of Stanley Cohen and Annie Chang, in constructing functional DNA from two different sources. Such chimeras, as they became called, were initially engineered by splicing together segments from two different plasmids (extrachromosomal DNA found in some bacteria) from the Escherichia coli bacillus. The chimera was then inserted into E. coli and was found to replicate and, equally significant, to express traits derived from both plasmids.

Development after 1973 was so rapid that by 1976 it had occurred to Boyer and a number of other workers that recombinant DNA could be used to produce such important proteins as insulin, interferon, and growth hormone in commercial quantities. Consequently in 1976 he joined with financier Robert Swanson to invest $500 each to form the company Genentech, which went public in 1980.

Despite successfully developing techniques for the production of somastatin in 1977, insulin in 1978, and growth hormone in 1979, the position of Genentech was far from secure at the beginning of 1981 with the emergence of competition from a number of rival companies and legal problems concerned with the ownership of genes.