The study used a district-level data from 2008-2012 to examine socio-economic factors affecting academic performance of pupils in food insecure district of Garu-Tempane, Upper East Region. The study explored the possible correlation between selected factors like age (years), type of marriage, religion, number of dependent, type of residence/domicile, type of dwelling, occupation and highest qualification of parent/guardian as independent variables and academic performance as dependent variable. A quasi-experimental design was used in selecting 360 pupils both from participating and non-participating public primary schools with similar socio-economic characteristics in Garu-Tempane District. The study revealed a causal link between school feeding program and academic performance as the participating schools' pupils had an improved academic performance. Again, Pearson Product Moment Correlation coefficients for socio-economic variables and academic performance results showed positive significant correlations (p<0.05) with type of marriage, (r=0.69), number of dependent, (r=0.193) and type of residence/domicile, (r=0.188). The study therefore recommended that the school feeding programs' sustainability should be well-targeted not only on the basis of food insecurity but through a more rigorous in-depth socio-economic survey and vulnerability mapping with a view to scaling-up of the program in food deficit areas to incorporate more schools.