Although some politics and international relations discourses continue to maintain that there is a causal link between secularism and political modernity, religious studies, anthropology, and history research over the past decade has been rather merciless in debunking this idea as one of the tropes of Western imperialism. This article considers at how Japanese political thinkers of the eighteenth and nineteenth centuries engaged this trope, and how that engagement contributed to the particular relationship between religion and governance that emerged in the modern Japanese empire (1868–1945). The article argues that developments in the Confucian political thought of the Tokugawa shogunate (1603–1868), particularly in the works of Ogyū Sorai (1666–1728) and Aizawa Seishisai (1792–1863), contributed significantly to the capacity of Japanese thinkers and politicians to creatively engage the role of religion in Western imperialism during the nineteenth and twentieth centuries.