Hideki Yukawa (1907-1981) was awarded the Nobel Prize for Physics in 1949 for the meson theory research and became the first Nobel laureate in Japan. Sin-itiro Tomonaga (1906-1979), one of Yukawa’s classmates at Kyoto Imperial University, became the second Japanese Nobel laureate for Physics in 1965 together with J. Schwinger and R. P. Feynman for their research on the renormalization method in quantum electrodynamics. In this paper, we focus on the roles of symbolic and actual leaders of “Yukawa” and “Tomonaga” in the management of physics or science systems in postwar Japan. Our special focus will be on the effective combination of the two roles as well as the two separate ones for managing physics or science in the cases of the establishment of Yukawa Hall at Kyoto University and Institute for Nuclear Study at Tokyo University. In the limelight after the Nobel Prize for Physics, the symbol “Yukawa” had the attention of Japanese people hoping the rebirth of their own country by the development of science and technology. The “Yukawa Boom” helped to facilitate the new science policy in the reconstruction of Japanese society. In that mood, “Tomonaga,” who returned from the Institute for Advanced Study at Princeton, acted as a leader to make the new science system including the establishment of the new type research institutions and the future policy on nuclear sciences. Uniting the roles “Yukawa” and “Tomonaga,” the two central scientists could make an effective management of physics or science policies in postwar Japan.