In this study, we use secondary data to look at the factors that affect mathematics and reading achievement among primary school children in Botswana and Lesotho. The data were gathered on 3,276 sixth grade students in Botswana nested in 606 classrooms and 3,155 sixth grade students in Lesotho nested in 250 classrooms. We used hierarchical linear modeling (HLM) to analyze the data. Results indicated that mother’s education, teacher’s content knowledge, teacher gender, and the number of livestock owned were some of the factors that impacted students’ academic achievement in mathematics and reading in primary school. Implications of these findings on mathematics and reading in primary education in Botswana and Lesotho are discussed.