The aim of this study is to identify the explanatory factors of the difference in school performance between pupils of the francophone and anglophone education subsystems at the primary school level in Cameroon. Using data from the Programme d’Analyse des Systèmes Educatifs de la CONFEMEN (PASEC) collected in 2014, the study employs a two-stage modelling approach. First, the estimation of educational production functions by OLS shows that student characteristics, as well as the school context, are factors that determine the academic performance of students in the anglophone and francophone subsystems. Secondly, the comparison of students’ academic performance between the educational subsystems using the Oaxaca-Blinder (1973) decomposition technique showed that at the end of the primary school year, more than 100% of this difference is explained by factors explained in both mathematics and language. The share of unexplained factors, however, does not suggest any discrimination in school performance against the anglophone sub-system. This calls for policy makers to consider their role in reducing the various sources of inequality among students of all kinds.