This paper addresses the formation of the law and legal system of Japan during the Meiji Restoration in the nineteenth century in the context of the historical relationship between religion and the state in Japan. I will examine how the post-World War II restructuring of Japan, led by Allied powers, affected the Japanese legal structure, Constitution, Supreme Court, the role of the emperor, and the concept of individual rights, specifically religious freedom. Despite efforts by the Allied powers to enforce the separation of church and state though the inclusion of such principals into the revised Japanese Constitution, the Japanese Supreme Court has attempted to mediate the text of the Constitution in an effort to reconcile the prevalence of Shinto religion in everyday Japanese life. Using the two most important cases regarding religious freedom between 1975 and 2000, this analysis provides evidence that the Japanese Supreme Court has been a pivotal actor in interpreting the scope of the new Constitution’s provision for the separation of church and state in Japan.