The Turkish Grand National Assembly was debating on the foundation of the first theology faculty at Ankara University when a representative warns the minister of education about the decision and states “the struggle between mektep (school) and madrasa (Muslim religious school) and the conflict between science and religion have caused bloody stages of history not only in the history of our country but also in the history of humankind…”(T.B.M.M., 1949, 20-3, pp. 279-280). As the quote sets forth, religious education is a long-standing issue in Turkey, starting from the mektep-madrasa conflict in the late Ottoman Empire to the foundation of theology faculty in the early years of the Turkish Republic. This issue is closely related to the predicament of modernity and Islam in Turkey; it involves the role and place of Islam in political and social life that continues to be at the center of heated debates even today. The recent revival of academic Islamic studies with its diverse scholarship and Islam’s increasing presence in political and social discourse in contemporary Turkey requires a reconsideration of the history of the origin of these debates. This paper discusses this controversial character of higher religious education in Turkey, problematizing the mektep-madrasa conflict in the late Ottoman Empire and the historico-political developments in the early republican era that led to the foundation of the first theology faculty in 1949. Based on a textual analysis of historical texts, governmental documents, and an examination of institutional organization of A.U. Divinity School, this study analyzes the significance of the faculty and locates the faculty’s scholarly approach to Islamic studies in Turkish socio-political history.