Given recent evidence of rising levels of social segregation in European countries, this study uses standardized data from the Program for International Student Assessment (n = 171,159; 50.5% male) to examine the extent to which education systems in Europe are socially segregated and whether social segregation in the school system affects achievement gaps between students of different social origin. Results suggest that the degree of social segregation within education systems varied substantially across countries. Furthermore, multilevel regression models indicate that the effect of socioeconomic status on student achievement was moderately but significantly stronger in more segregated education systems, even after controlling for alternative system-level determinants of social inequality in student achievement. These findings provide original evidence that social segregation in education systems may contribute to the intergenerational transmission of educational (dis)advantage and thus serve to exacerbate wider problems of socioeconomic inequality in Europe.