Gender and socio-economic background of a pupil have been linked to school opportunities and achievement. However, their effects vary across cultures and environments. This paper examines gender parity in primary schools in Kenya and factors that explain differential performance in mathematics and reading including gender. The paper also presents an analysis of internal efficiency and gender equity in primary schools in Kenya and empirical evidence on what explains achievement in mathematics and reading scores. Gender differentials are manifested in schooling performance and that various gender related and socio-economic variables affect pupils’ performance in mathematics and reading differently. Overall, boys perform better than girls in both mathematics and reading. Teachers’ competencies in subject matter has positive impact on respective subjects, that is reading and mathematics.. Emerging policy implications include need to put more emphasis on the professional development of teachers in mathematics and reading; and reading skills for both teachers and students. Pedagogical interventions in Kenya’s basic education should focus on improving performance of girls in both mathematics and reading; provision of basic schooling sanitation facilities should be increased; and general reduction in poverty levels would lead to the improvement in schooling performance.