Improving education quality in Sub-Saharan Africa is essential for fostering economic and social development. This study investigates the determinants of primary school students’ academic performance using the PASEC database and applies a multilevel model that accounts for endogeneity to examine individual, family, and school-level factors. Findings reveal that individual and family-related characteristics explain 69% of the variation in achievement. Late school entry, grade repetition, gender, and high engagement in extracurricular activities negatively influence performance, whereas socioeconomic status and parental literacy exert positive effects in nearly half of the countries analyzed. At the school level, better access to textbooks, teaching materials, and adequate infrastructure significantly improves learning outcomes. In contrast, teacher-related factors such as working conditions and training duration do not exhibit a significant impact. These results underscore the importance of integrated education policies that address individual, family, and school-level barriers to enhance learning outcomes in Sub-Saharan Africa, providing valuable guidance for policymakers.