OBJECTIVES: To assess space-time trends in malnutrition and associated risk factors among children (<5 years) in South Africa. DESIGN: Multiround national panel survey using multistage random sampling. SETTING: National, community based. PARTICIPANTS: Community-based sample of children and adults. SAMPLE SIZE: 3254 children in wave 1 (2008) to 4710 children in wave 5 (2017). PRIMARY OUTCOMES: Stunting, wasting/thinness and obesity among children (<5). Classification was based on anthropometric (height and weight) z-scores using WHO growth standards. RESULTS: Between 2008 and 2017, a larger decline nationally in stunting among children (<5) was observed from 11.0% to 7.6% (p=0.007), compared with thinness/wasting (5.2% to 3.8%, p=0.131) and obesity (14.5% to 12.9%, p=0.312). A geographic nutritional gradient was observed with obesity more pronounced in the east of the country and thinness/wasting more pronounced in the west. Approximately 73% of districts had an estimated wasting prevalence below the 2025 target threshold of 5% in 2017 while 83% and 88% of districts achieved the necessary relative reduction in stunting and no increase in obesity respectively from 2012 to 2017 in line with 2025 targets. African ethnicity, male gender, low birth weight, lower socioeconomic and maternal/paternal education status and rural residence were significantly associated with stunting. Children in lower income and food-insecure households with young malnourished mothers were significantly more likely to be thin/wasted while African children, with higher birth weights, living in lower income households in KwaZulu-Natal and Eastern Cape were significantly more likely to be obese. CONCLUSIONS: While improvements in stunting have been observed, thinness/wasting and obesity prevalence remain largely unchanged. The geographic and sociodemographic heterogeneity in childhood malnutrition has implications for equitable attainment of global nutritional targets for 2025, with many districts having dual epidemics of undernutrition and overnutrition. Effective subnational-level public health planning and tailored interventions are required to address this challenge.