This paper examines the extent to which factors related to pupil, home, teacher and school background influence pupil achievement in mathematics and reading literacy in Botswana, one of the fourteen countries represented in the SACMEQ II investigation. The process of developing and examining a hypothesized causal model for explaining pupil achievement in Botswana was presented in detail to enable future researchers to replicate the structural equation modelling (SEM) procedures for each of the remaining thirteen countries. School location, family socio-economic status (SES), total school resources and class repetition were found to be the most important factors associated with pupil achievement in Botswana. The direct and indirect effects of the background characteristics on pupil achievement were explored and examined. As the analyses enabled causal effects to be identified, a series of specific intervention strategies were recommended for priority implementation in order to enhance future pupil achievement in Botswana.