This study investigates the influence of missionary education on the evolution of formal schooling in Nigeria from the nineteenth century to the present. Utilising a qualitative historical research design with a secondary method approach, the study incorporates primary sources (missionary records, colonial documents, and contemporary accounts), secondary sources (scholarly monographs and articles), and official publications. The theoretical approach utilised dependency theory to investigate structural disparities. The results show that missionary education caused long-lasting differences between northern and southern Nigeria, set up patterns of gender inequality, and made religious instruction a part of formal schooling in ways that continue to cause arguments. At the same time, the results show that Africans had a lot of power. Liberated returnees, local converts, and communities all played a role in creating and negotiating missionary education. The study finds that the legacy of missionary education is mixed. It helped set up formal schools, but it also created disparities and institutional tendencies that are still big problems. Suggestions include focused funding for northern educational infrastructure, policy changes to promote gender equality, clearer definitions of the role of faith-based organisations in education, changes to the curriculum to include indigenous knowledge, and future research that uses comparative, oral history, and intersectional methods.