Religious intolerance remains a major driver of violent extremism, social displacement, and economic stagnation across Africa. This paper analyzes the structural causes of religious friction, focusing on its devastating effects on national security and regional development. By reviewing recent historical data and contemporary regional conflicts, the study evaluates how political manipulation and weak governance exacerbate sectarian identities. The findings indicate that religious intolerance severely undermines human rights and stunting GDP growth. The paper offers actionable, multi-layered solutions, emphasizing the critical role of inclusive education, legal enforcement of secularity, and grassroots interfaith dialogue.