This research examined the influence of private and public schools on pupils‟ proficiency in mathematics and English language subjects. The theoretical model that supported the study was the bioecological model of human development. The sample comprised 16,481 Primary 3 and 14,495 Primary 6 pupils from 448 and 426 schools respectively. The research design was a descriptive cross-sectional survey. Schools were sampled using a stratified random sampling technique. Data were analyzed using a multilevel modeling technique. The significance or otherwise of the influence of school type on pupils‟ proficiency in both subjects was assessed at p < 0.001. The results showed that many pupils performed below the minimum competency level in both subjects uniquely because they attended public schools. Conversely, many pupils were found to be proficient in both subjects exclusively because they attended private schools. The research findings suggest that the type of primary schools pupils attend in Ghana significantly mattered for their academic success and the progression from one grade-level to another. The results imply that learning opportunities are not equal for all pupils. This has implications for the effective implementation of the primary school curriculum in the country. To improve upon the academic achievement of primary school children in Ghana, first, there is the need to eliminate the achievement gap between private and public schools.