Mathematics literacy is essential for all further learning and future careers of students, therefore, the poor performance of Botswana Junior Certificate learners in Mathematics is very concerning. This study adopted an exploratory research design which utilized the TIMSS 2015 data to analyse student and school variables responsible for the differentials in mathematics achievement. TIMSS represents Trends in International Mathematics and Science Study. The socio-economic status of students’ parents, location of schools, and students’ gender in Botswana Junior Certificate students’ mathematics achievement were explored through the Multilevel (Hierarchical) Linear Model (HLM) to predict the mathematics achievement of the students. The data used for this study was derived from that of the tenth grade Botswana students; a total of 5964 (female = 3030, male = 2934) Botswana tenth graders from 159 schools who participated in TIMMS 2015.Based on the findings of the study, recommendations were made on some interventions to help improve students’ self-efficacy and confidence in mathematics.