This paper aims to compare the history of science in Choson and Japan during the "modern" period. First, the problems of defining the word "modern" is discussed in history and history of science. Second, three characteristics during modern period in Choson and Japan was compared: the introduction of Western science and its assimilation; the popularization and institutionalization of science; and industrialization. Third, shirak 實學 in two countries was compared. Shirak meant practical knowledge that had actually contributed to the development of industry and society in Japan while it had largely remained as another scholastic learning with little practice in Choson. Lastly, Hong Daeyong's and Shizuki Tadao's world system were discussed to illustrate how these two East Asians endeavored to understand the Western world system with Confucian background.