The paper uses multilevel analysis procedures to examine individual- and group-level learning barriers that have the greatest impact on pupil achievement in Uganda. The data for this study were collected in 2014 among 2711 Grade 6 pupils attending 82 schools in two rural districts of Iganga and Mayuge in Uganda. Data used in this paper are part of a larger study which sought to examine the schooling patterns, as well as the quality of education received by children living in rural settlements in Uganda. Among the learning barriers with the greatest impact on pupil achievement at the individual-level were lack of parental involvement, lack of pre-primary school attendance, grade repetition, and lack of basic learning resources such as writing materials. At the school-level, the barriers with the most impact on pupil achievement were lack of teacher lesson preparedness, lack of teacher-classroom support by subject advisors, distance between school and teachers’ place of residence, lack of basic classroom resources, and whether or not the teacher kept pupil learning progress records. Implications of the findings for policy and practice are outlined.