Bolonkin was born in Perm. He got a higher secondary education in aviation engineering from Perm Aviation College, receiving its diploma in 1952. His higher education resulted in a master's degree in aircraft from Kazan Aviation Institute in 1958, a master's degree in mathematics from Kiev University in 1963, a doctorate in aerospace engineering from the Moscow Aviation Institute in 1964, and a habilitated doctor degree in cybernetics and mathematics from Leningrad Polytechnic University in 1971. He worked at the Antonov aviation design company as a senior engineer and head of the aerodynamics group, participating in the design of aircraft from the An-8 to the An-124, and at the Glushko rocketry company, participating in the design of rocket engines, and lectured at the Moscow Aviation Institute, the Moscow Aviation Technology Institute, and the Bauman Moscow State Technical University. In 1972 he was arrested by the KGB for dissemination of an underground dissident newsletter, listening to the Voice of America and reading and disseminating works by Andrei Sakharov and Aleksandr Solzhenitsyn. Bolonkin was sentenced to 4 years in a labour camp and 2 years in exile in Buryatia. Shortly before his sentence of exile ended Bolonkin was given a sentence of 2 years in a labour camp on a charge of stealing state property. For 15 years he was tortured, imprisoned, and exiled in Siberia. In 1981 Sakharov appealed for international support to have him freed. In April 1982 he made a televised recantation that Amnesty International ascribed to threats of beatings and rape. In 1987, during the early perestroika, he was released and gained entry to the United States as a political refugee. In the United States he has lectured at New Jersey Institute of Technology and worked at NASA as a senior researcher and in the scientific laboratories of the US Air Force as a senior research fellow of the National Research Council. He subsequently worked in Israel as chief scientist at the Strategic Solutions Technology Group.
Bolonkin is a member of the Board of Directors of the International Space Agency and chairman of the space flights section. He is also a member of the advisory board of the Lifeboat Foundation and its space settlement board, and the founding President of the International Association of Former Soviet Political Prisoners and Victims of the Communist Regime and co-founder and co-chair of ARA, an organization for the civil and human rights of Russian-Americans.