This article examines the effect of school choice and residential choice on schools’ mix and academic performance using the Korea Education and Employment Panel (KEEP). The results are as follows: In regions under implementation of the high school standardization policy, schools were not segregated by academic performance. However, school segregation by regional, social and economic status (SES), and household income persisted in regions under the high school standardization policy. In contrast, school segregation by academic performance and by regional SES in regions under the high school non-standardization policy was higher than in regions under the high school standardization policy. When the school choice system was reinforced, school segregation was found by academic performance in the standardized regions: strengthening the school choice system had the positive effect of increasing the probability of good school assignment in regions under the non-standardization policy, but at the same time it had the negative effect of raising the probability of poor school assignment in residential areas with low SES and household income.