Using data from the China Education Panel Survey (CEPS), this study empirically examines the association between internal migration and child health through an investigation of health disparities between migrant children and left-behind children in China. The results show that, in comparison with being left behind, migrating with parents significantly improves children’s self-reported health, height-for-age z-score (HAZ) and BMI-for-age z-score (BAZ), and reduces their frequency of sickness. These findings remain robust to a suite of robustness checks. Furthermore, the health effects of internal migration are more prominent for children with a rural hukou compared with urban ones. Although migrant children are more likely to experience teacher discrimination, they have higher levels of parental care, family relationships, and peer relationships relative to their left-behind counterparts, which indicates possible mechanisms behind the association between children’s migration and health. Our findings underline the importance of policy improvement and evidence-based interventions aiming at reducing involuntary parent-child separation and facilitating the development in health of disadvantaged children in developing countries like China.