This paper analyzes the critique of Neo-Confucianism by the Japanese Jesuit Brother Fabian Fukansai (c. 1565–1621) in the Myōtei Dialogues (Myōtei Mondō 妙貞問答) (1605), as well as Fabian’s later critique of Christianity. It clarifies the author’s understanding of Neo-Confucian theory and his apology for Christianity by analyzing his explanation of the Great Ultimate (Tai’kyoku/Taiji 太極) and Principle (ri/li 理), which Fabian sees as nothing but an expression of Buddhist monistic mentalism. It also demonstrates that his explanations of the Great Ultimate and Principle have a crucial flaw: they do not sufficiently explain Zhu Xi’s metaphysics, which tried to make the immanent and transcendental characteristics of the Great Ultimate and Principle compatible. This is because Fabian addresses only the elements of “local” religions including Neo-Confucianism with novel keywords that support the framework of Christian Creationism and the Anima Rationalis theory. However, his later work Deus Destroyed (Ha Daius 破提宇子), written after he had rejected Christianity, overturned his former claim by accepting the Neo-Confucian concept of Principle. Fabian’s works are a historical example showing the potential limits of a confrontational approach toward other religions.