In this study we present evidence on the impact of individual and school characteristics on grade 6 pupil achievement using a rich dataset from Uganda. We deal with an important selection issue in Uganda—the non-random allocation of children into schools due to a high school dropout rate. We do so by employing a combination of fixed effects and including variables capturing sample selection. Our empirical results reveal that teacher training is important for improving school performance. Indeed, having the mandatory two years of teacher training is more important than a teacher’s own cognitive ability. On the other hand, access to classroom resources raise children’s cognitive outcomes—a child having either an own place to sit significantly impacts on learning outcomes. Consequently, efforts to improve children’s cognitive outcomes should concentrate on providing in service teacher training as well as ensuring that classrooms are properly furnished.