Rutter grew up in Malad, Idaho. He attended high school there until the age of 15, at which point he spent a year at Brigham Young University. After his year at Brigham Young, Rutter claimed to be 18 and joined the navy, serving until the end of World War II. He then was admitted to Harvard University and received his B.A. in both biochemistry and chemistry in the winter of 1949. He returned to the University of Utah, working with Gaurth Hansen on studies of metabolism and earned his M.S. in biochemistry in 1950. Rutter received his Ph.D. in biochemistry from the University of Illinois in 1952. He took up a postdoctoral position at the University of Wisconsin, where he studied enzyme chemistry, and his interests led him to take a second postdoctoral position at the Nobel Institute in Stockholm before accepting a teaching position at the University of Illinois. In 1965 he decided to move to Seattle and take a position at the University of Washington, where he learned genetics and began to research mechanisms of gene transcription. Three years later he moved again, this time accepting the chair of the biochemistry department at the University of California at San Francisco (UCSF). Chiron Corporation was founded in 1981 by Rutter, Valenzuela, and another researcher, Edward Penhoet. In 2006 Chiron was acquired by Novartis International.