In January 1944, Kistiakowsky joined the Manhattan Project, replacing Seth Neddermeyer as head of the implosion program. He oversaw 600 people on the development of a triggering device to detonate the atomic bomb-explosive lenses that uniformly compress the plutonium sphere to achieve critical mass.
Kistiakowsky returned to Harvard at the end of World War II and divided his time between teaching and advising several US administrations on arms control and foreign policy. He served on the President's Science Advisory Committee between 1957 and 1964, and as the Special Assistant to the President for Science and Technology from 1959 to 1961. In 1958, Kistiakowsky was a member of the US delegation to Geneva, where the US and USSR discussed how to minimize the danger of a surprise nuclear attack.
Kistiakowsky was concerned with public policy and the allocation of government resources. He worked to influence these arenas through the National Academy of Sciences (NAS), serving as chairman of its Committee on Science and Public Policy from 1962 to 1965, and as vice-president of NAS from 1965 to 1973.
Kistiakowsky became increasingly doubtful about the possibility of changing politics from within the administrative channels in Washington. In 1968, Kistiakowsky severed his connections with the Pentagon to protest US involvement in Vietnam. After retiring from Harvard as professor emeritus in 1972, Kistiakowsky became even more involved in political activism in the areas of de-escalating the arms race and banning nuclear weapons. In 1977, he assumed the chairmanship of the Council for Livable World, campaigning to de-escalate the arms race and reorient the domestic political agenda.
Kistiakowsky received numerous awards throughout his lifetime for his work in science and in politics, including the Presidential Medal of Freedom and the Joseph Priestly Award of the American Chemical Society.
George Bogdan Kistiakowsky died on December 7, 1982.