Internal rural–urban migration and its implications for children’s education are critical factors in understanding China’s rapid pace of urbanization. However, previous studies relying on cross-sectional data often treat migration as a one-off event, oversimplifying the migration process. This study uses data from the China Family Panel Studies (CFPS) for 2010–2018, along with a newly developed analytic strategy, to estimate the effect of children’s migration trajectories on their educational outcomes. Using panel data, this study examines various migration trajectories by considering the directions and frequencies of migrations. Results show the heterogeneities among migrants. First, while permanent migration does not adversely affect children’s education, return migration and multiple migrations lead to increased educational penalties. Beyond the segregation between urban and rural areas, the findings highlight the significant disadvantages linked to migration between provinces, which profoundly affect educational outcomes compared to migration within provinces. Finally, the findings suggest there are gender differences in the impact of migration experiences, with boys facing greater challenges to their education.