The article deals with the problem of the relationship between philosophy and theology within the confessional nature of university theological education. This issue is of particular relevance in the light of the formation and development of national university theology. The nature and content of academic disciplines, understanding of goals and objectives in the training of specialists in theology depends on the solution of this problem. Ideas about theology can be different, so clarifying this issue will allow creating a balanced system of theological education in the framework of secular educational institutions. This issue is considered in relation to Christian theology.