This article discusses the treatment of religion in Japanese education in the post-World War Two period. During the Allied Military Occupation, Japan adopted the principle of the separation of state and religion as a means to democratize the totalitarian, ethno-nationalistic education system of pre-1945. The case of Germany is also dealt with here for a comparison to explore how the similar purpose fitted in with the reform debates on the German education system during the Occupation. The purpose of this article is to trace the geneses of the current treatment of religion in Japan education. Thus, the prime interest of this article is not to discuss the argument that the demise of religious instruction might have created a basis for the decline of morality among children. Nor does the article address a question whether nor not emphasis on instruction in religion might cultivate a sense of national identity among the youth. Instead, this article tries to investigate historical backgrounds which, I argue, have helped taboo such discussions about the values and roles of religious education of these kinds in post-war Japan.