I use anthropometric scores from two nationally representative surveys in South Africa to examine the comparative changes in urban and rural children’s health over the 15 years post-Apartheid. I find that the urban advantage in children’s health disappears despite urban children retaining considerable advantages in average household socioeconomic status. I then explore several explanations for this pattern common in the urbanization literature, including the growth of particularly vulnerable urban populations, such as migrants and residents of informal areas, and/or the deepening of household poverty in the poorest urban areas. I do not find evidence of deteriorated circumstances for the urban poor, but I do find evidence that rural-urban migrants have begun to show a health disadvantage. However it appears to be related to the relative poverty of rural-urban migrants. I then follow the Dinardo Fortin Lemeiux decomposition method to explore relative shifts in the distribution household wealth and parental education in urban and rural households. I find that the differential gains are likely due to large improvements made by very poor rural households rather than deterioration in urban wellbeing.