In the context of modern science, Religious Studies is a branch of science that has been emerged in the “structure of plausibility” of Western traditions. As a scientific knowledge, Religious Studies differs from Theology and Philosophy in which scholars, like Friedrich Max Müller, applied the scientific and empirical method in their research. In this regard, Religious Studies would be a part of “positivistic sciences”. In applying those scientific approaches and methods at the Islamic Studies which has been held in Islamic universities like UIN, IAIN, and STAIN, and other high educations in Indonesia will cause epistemological and axiological problem. Inter-relationship between subject and object is a main obstacle of this discipline. The method of Western sciences is constructed by empirical approach an sich while Islamic scientific tradition reflected by conviction which proved by empirical approach known as sui generis cum doctriner method. According to that problem, by applying Karl Manheim’s ‘structure of plausibility’ and Foucault’s ‘archaeology of knowledge’, this article attempts to explore the roots of epistemology of Religious Studies in Islamic higher education institution. Furthermore, this article also attempts to introduce the analysis model of Religious Studies in the Islamic institution namely elenctic method. This method assumes that religious phenomena can be analyzed by two phases, firstly by describing all of religious phenomena as what is understood by its adherents, and secondly by analyzing those religious phenomena with theoretical approaches