Johnson was born in 1931 in Phoenix, Arizona. He earned a BA in economics in 1953 and an M.A. and a Ph.D. in political science in 1957 and 1961 respectively. Both of his advanced degrees were from the University of California, Berkeley. Johnson met his wife Sheila, a junior at Berkeley, in 1956, and they were married in Reno, Nevada in May 1957.
During the Korean War, Johnson served as a naval officer in Japan. He was the communications officer on a ship (the LST 883) "tasked with ferrying Chinese prisoners of war from South Korea back to North Korean ports." He taught political science at the University of California from 1962 until he retired from teaching in 1992. He was best known early in his career for his scholarship on the subjects of China and Japan.
Johnson set the agenda for 10 or 15 years in social science scholarship on China with his book on peasant nationalism. His book MITI and the Japanese Miracle, on the Japanese Ministry of International Trade and Industry was the preëminent study of the country's development and it created the subfield of what could be called, the political economy of development. He coined the term "developmental state". As a public intellectual, he first led the "Japan revisionists" who critiqued American neoliberal economics with Japan as a model; their arguments faded from view as the Japanese economy stagnated in the mid-90s and beyond. During this period, Johnson acted as a consultant for the Office of National Estimates, part of the CIA, contributing to analysis of China and Maoism.
Johnson was elected a Fellow of the American Academy of Arts and Sciences in 1976. He served as Director of the Center for Chinese Studies (1967–72) and Chair of the Political Science Department at Berkeley, and held a number of important academic posts in area studies. He was a strong believer in the importance of language and historical training for conducting serious research. Late in his career he became well known as a critic of "rational choice" approaches, particularly in the study of Japanese politics and political economy.
Johnson is, perhaps, best known today as a sharp critic of American imperialism. His book Blowback (2000) won a prize in 2001 from the Before Columbus Foundation, and was re-issued in an updated version in 2004. Sorrows of Empire, published in 2004, updated the evidence and argument from Blowback for the post-9/11 environment, and Nemesis concludes the trilogy. Johnson was featured as an expert talking head in the Eugene Jarecki-directed film Why We Fight, which won the 2005 Grand Jury Prize at the Sundance Film Festival. In the past, Johnson has also written for the Los Angeles Times, the London Review of Books, Harper’s Magazine, and The Nation.