The distribution of children in different school-types and regions in Pakistan suggests that access and opportunities in education are not evenly accessible for many children. Segregation at school level is an important concern for equity and social justice because the adverse effects of segregation increase the pre-existing gap in opportunities between rich and poor, preventing the disadvantaged children from equal access to better life and success opportunities. This paper presents an analysis of segregation by poverty and pupil performance between schools, with a comparison of private and government schools in Pakistan. The data obtained for this study is from the Annual Status of Education Report 2014 survey of households and schools. The analysis includes 27,979 children aged 5-16 years for whom the information could be linked with their schools, and parents' socio-economic status. Segregation levels have been assessed using the Gorard Segregation Index. The results show that segregation by academic performance is higher than segregation by poverty, and segregation by poverty is higher in the private sector compared to government schools, whereas segregation by performance is greater in the government schools. A regional level analysis shows that segregation in urban areas is higher in both school types compared to rural areas. In addition to insisting on full attendance for children of school age, the government should work towards decreasing segregation in the state sector, perhaps also involving an increase in the number of schools maintained, and therefore reducing the need for cheap private provision.