Inequality in the educational transition by family’s socioeconomic status (SES) can be decomposed into part associated with gaps in academic achievement (primary effects) and part associated with social processes shaping gaps in preferences and choices beyond academic achievement (secondary effects). We examine how family SES gaps in transitions to high school and college education, as well as the importance of primary and secondary effects, have changed across birth cohorts born between 1950s and 1999 in South Korea, using data from Korea Education and Social Stratification and Mobility and Korean Education and Employment Panel. Our analyses reveal three key findings. First, family SES gaps in educational transitions to colleges were shaped primarily by secondary rather than primary effects. The trends were also largely influenced by changes in secondary effects. Second, family SES gaps in the transition to selective 4-year colleges, proxied by 4-year colleges located in Seoul, is predominantly shaped by primary effects. Third, the importance of academic achievement has decreased for the transition to a less selective stage (e.g., transition to junior college or higher), while it has increased for the transition to a more selective stage (e.g., entry into a selective college). The relative contribution of primary effects has also generally increased in recent birth cohorts. Our study suggests that academic and polity attention to inequality of educational opportunity should be extended to inequalities in cultural, institutional, and non-cognitive aspects of students’ lives from the narrow focus on gaps in academic achievement.