Rural-urban migrants, though facing unique social and institutional constraints, remain a largely overlooked population in research on health inequality in China. This study applies the inequality of opportunity (IOp) framework to investigate health inequality among children in China. Instead of comparing only urban and rural children, we include rural-urban migrants. Drawing upon three waves of a nation-wide survey, we find that migrant children in China remain disadvantaged in terms of health when compared to urban and rural children. The decomposition of the determinants indicates that while the direct influence of hukou, China’s household registration system, on IOp in health is low and has decreased, particularly between 2007 and 2013, one’s province of residence still matters. Parental health contributes substantially to IOp in health, which likely is an indirect effect of hukou that creates barriers for migrant parents in regard to accessing healthcare. The policy implication of these findings is that although the direct influence of hukou has decreased, when coupled with the continued lack of local government support for the welfare of migrant workers, it perpetuates health inequalities.