The article chronicles the history of emergence of theology as educational subject and scientific discipline in the Russian higher education and the academic studies since 1992. Theology as educational subject appeared not as the project suggested by religious organizations, but rather as an initiative of the state educational bodies and the institutions of higher education as the result of the institutional collapse of the structure of scientific atheism in 1991. The article provides historical information on the development of the attitude of hierarchy of Russian Orthodox Church to the idea of university theology and on the role of the Church in development of state theological educational standards, as well as in introducing theology into the list of scientific disciplines. The article then discusses the debatable issues of qualifying theology as a scientific discipline. Drawing upon Habermasian approach, the author examines the meaning of the secular status of university education and the scientific status of theology in social and philosophical perspectives.