The Central African Republic has been entangled in new cycles of conflict since the upsurge of the Seleka insurgency in December 2012. Although a number of reasons account for the violent nature of the conflict and its protracted nature, sectarianism appeared to be the most glaring and leading driver of the conflict. The dominance of the Christian majority over the Muslims in every aspect of life, the questionable Central African citizenship of CAR Muslim population have led to overt discrimination against the minority Muslim population. This discrimination on religious lines adds to ethnic discrimination by various CAR leaders who offer preferential treatment to members of their ethnic groups through appointments to top government and military positions, to the detriment of the other tribes, breeding ethnic division. Applying the Protracted Social Conflict theory, this article attempts to investigate into how sectarianism contributed to the protraction of the CAR conflict from 2012–2020. The paper applies a qualitative method of analysis to investigate the sectarian roots of the 2012 conflict in the CAR. Data collection and analysis involved secondary sources in the form of books, scientific journal publications, reports and other relevant internet sources to answer the central question in the research.