Since the mid-1990s, important education policy changes, such as the growth of Direct Subsidy Scheme (DSS) schools and the reform of the medium of instruction (MOI) policy, have been made in Hong Kong. Little is known about their impact on school segregation and educational inequality. We address this issue using six successive cycles of the Trends in International Mathematics and Science Study data. We found evidence for rising levels of secondary school segregation in terms of family socio-economic status and mathematics achievement from 1995 to 2011, whereas segregation declined from 2011 to 2015. We speculate that the salience of the MOI policy in expediting the segregating tendencies of the DSS sector might explain a growing magnitude of the effect of family socio-economic status on academic achievement between 1995 and 2011, and the reversed direction of such trends between 2011 and 2015. Implications are discussed.