This paper examines the separation of church and state in the Philippines during the early American colonial period, contextualizing it within the process of American overseas expansion and considering it as one of the projects of imperial hegemony construction. After the Spanish–American War, the United States substituted Spain as the new colonial ruler of the Philippines, legitimizing its regime as the spread of ‘civilization’ to the Filipinos. On this basis, the Americans enacted laws guaranteeing religious freedom and introduced an American-style institution dealing with church–state relations. Beyond the legal and administrative initiatives, the new regime also constructed an official narrative of the transformation of political–religious relations in the Philippine that emphasized the absolute ‘difference’ between the American human rights principle, which guaranteed freedom of worship, and the Spanish theocracy, which was dedicated to the consolidation of privileges. By legislating the separation of church and state, buying up church properties, recognizing the equality of denominations, and constructing the official imperial narrative of church–state relations, the Americans hoped to ‘teach’ Filipinos that the ‘true’ belief was rooted in the inner convictions of individual Christians, not in the authority and coercion of the hierarchical church. By disciplining the construction of ‘difference’ under tutelary colonialism, the separation of church and state movement initiated by the American colonial government in the Philippines became an important source of imperial self-endowed legitimacy.