In this paper the author handles the issue of secularism in African context and shows that it is wrongly defined due to the use of European inherited or mimicked standards. He explains that, while Western perception places religion out of the field of science, the naturalized epistemology of African indigenous knowledge demonstrates that religion is one of the three components of African traditional science and that contrary to Western Christianity and to Islam, African traditional religion (ATR) involves a scientific content explaining rationally the relationship between God, man and the universe, and cultural contents necessitated by the need to apply the scientific religious principles within specific milieus. Moreover, ATR thus defined leads to a scientific and normative discourse of morality. Therefore, any strategy of secularization in Africa must first make the distinction between the scientific content of ATR and its cultural ones. It is thus obvious that, as far ATR is concerned, African governments must adopt non-secular policy vis-à-vis its scientific aspects, as it is the case for any science, and apply secularism only toward its cultural contents.