Pirsig was born on September 6, 1928, in Minneapolis, Minnesota, the son of Harriet Marie Sjobeck and Maynard Pirsig. He was of German and Swedish descent. His father was a University of Minnesota Law School (UMLS) graduate, and started teaching at the school in 1934. The elder Pirsig served as the law school dean from 1948 to 1955, and retired from teaching at UMLS in 1970. He resumed his career as a professor at the william Mitchell College of Law, where he remained until his final retirement in 1993.

Because he was a precocious child with an IQ of 170 at age nine, Pirsig skipped several grades and was enrolled at the Blake School in Minneapolis. At 14, in May 1943, Pirsig was awarded a high school diploma from the University of Minnesota's laboratory school, University High School (now Marshall-University High School) where he edited the school yearbook, the Bisbilla. He then entered the University of Minnesota to study biochemistry that autumn. In Zen and the Art of Motorcycle Maintenance, he described the central character, thought to represent himself, as being far from a typical student; he was interested in science as a goal in itself, rather than as a way to establish a career.

At 18, Pirsig enlisted in the United States Army in 1946 and was stationed in South Korea until 1948. Upon his discharge from the Army, he returned to the United States and lived in Seattle, Washington, for less than a year, at which point he decided to finish the education he had abandoned. Pirsig earned a bachelor's degree in 1950 from the University of Minnesota. He then attended Banaras Hindu University in India, to study Eastern philosophy and culture. At the University of Chicago, he performed graduate-level work in philosophy and journalism but he did not obtain a degree there. In 1958 he earned a master's degree in journalism from the University of Minnesota.

Robert Pirsig married Nancy Ann James on May 10, 1954. They had two sons — Chris, born in 1956, and Theodore (Ted), born in 1958.

In 1958, he became a professor at Montana State University in Bozeman, and taught creative writing courses for two years. Shortly thereafter he taught at the University of Illinois at Chicago.

Pirsig suffered a nervous breakdown and spent time in and out of psychiatric hospitals between 1961 and 1963. He was diagnosed with paranoid schizophrenia and clinical depression as a result of an evaluation conducted by psychoanalysts, and was treated with electroconvulsive therapy on numerous occasions, a treatment he discusses in his book, Zen and the Art of Motorcycle Maintenance. Nancy sought a divorce during this time; they formally separated in 1976 and divorced in 1978.

Guggenheim Fellowship: Awarded 1974. Field of Study: General Nonfiction.

1975, Outstanding Achievement Award conferred by the University of Minnesota.

On December 28, 1978, Pirsig married Wendy Kimball in Tremont, Maine.

In 1979, Chris Pirsig, who figured prominently in Zen and the Art of Motorcycle Maintenance, was fatally stabbed in a mugging outside the San Francisco Zen Center, at the age of 22. Pirsig discusses this incident in an afterword to subsequent editions of Zen and the Art of Motorcycle Maintenance, writing that he and his second wife Wendy Kimball decided not to abort the child she conceived in 1980 because he believed that this unborn child — later their daughter Nell — was a continuation of the life pattern that Chris had occupied.

On December 15, 2012, Montana State University bestowed upon Pirsig an honorary doctorate in the field of philosophy during the university's fall commencement. Pirsig was also honored with a commencement speech by MSU Regent Professor Michael Sexson. Pirsig was an instructor in writing at what was then Montana State College from 1958–1960. In Zen and the Art of Motorcycle Maintenance, Pirsig writes about his time at MSC as a less than pleasurable experience due to the teaching of philosophy at the agricultural college. Pirsig said that this limited his ability to teach writing effectively, as well as to develop his own philosophies and literature. Due to frailty of health, Pirsig did not travel to Bozeman in December 2012 from his residence in Maine to accept the accolade.

While doing laboratory work in biochemistry, Pirsig became greatly troubled by the existence of more than one workable hypothesis to explain a given phenomenon, and that the number of hypotheses appeared unlimited. He could not find any way to reduce the number of hypotheses—he became perplexed by the role and source of hypothesis generation within scientific practice. The question distracted him to the extent that he lost interest in his studies and failed to maintain good grades. Finally, he was expelled from the university.

Pirsig died aged 88, at his home in South Berwick, Maine, on April 24, 2017, after a period of failing health.