There has been a recent, rapid de facto privatization of education in many African countries, as the number of private secondary schools operating in the region grew. The majority of these schools are "low-cost" private schools where tuition and fees are set as low as possible to cover operating costs and still generate profit. Proponents of low-cost private schools argue that these schools have proliferated in impoverished areas to meet unmet demand for access to education and where private schools may offer better quality than locally available public schools. Theories of inequality of educational opportunity suggest that if private schools offer better quality education, students from more advantaged families will be more likely to enroll at these institutions, potentially exacerbating educational inequality in the region. This analysis uses data from a school-based longitudinal survey, the Malawi Schooling and Adolescent Study, to examine socio-economic inequalities in the transition to secondary school and on-time enrollment in upper secondary. My findings indicate that youth from non-poor households are not only more likely to enroll in secondary school than poor youth, but they are also more likely to substitute enrollment in private schools for enrollment in second-tier government schools. Enrollment at private schools, however, does not yield schooling advantages; relative to both tiers of government secondary schooling, students who initially enrolled at private schools were the least likely to enroll on time in upper secondary school. These patterns suggest that these schooling circumstances may yield less segregation of opportunity than might otherwise be assumed.