Background: In South Africa, the occurrence of the double burden of malnutrition is on the rise at a household level predisposing children and their mothers to negative health outcomes. However, few studies have been conducted at a household level. Therefore, we studied a double burden of malnutrition using child-mother pairs in a rural setting. Methods: A cross-sectional quantitative survey was conducted among 508 child-mother pairs selected from primary schools using a multistage sampling in a rural Dikgale Health and Demographic Site in Limpopo Province, South Africa. Anthropometric measurements of children and mothers, and socio-demographic data were collected. WHO AnthroPlus was used to generate body-mass-index z-scores of children and the BMI was used to indicate overweight and obesity among the mothers. Mann Whitney test was used to compare the means of variables between sexes and age groups, while the prevalence of thinness and overweight/obesity were compared using a chi-square. Multivariate logistic regression with a stepwise backward elimination procedure, controlling for confounding, was used to determine the association between the thinness and overweight/obesity and the covariates. Results: Twenty five percent (25%) of the children were thin, 4% were overweight and 1% obese, while mothers were overweight (27.4%) and 42.3% obesity (42.3%) were observed among the mothers. The odds of being thin were higher in boys than in girls (AOR = 1.53, 95%CI: 1.01-2.35). Overweight/obese mothers were more likely to have thin children (AOR = 1.48, 95% CI: 1.01-2.18) and less likely to have overweight/obese children (AOR = 0.18, 95%CI: 0.07-0.46). Conclusion: A double burden of malnutrition was observed on a household level with thinness among children and overweight/obesity among mothers. A need to address the dual problems of undernutrition and rapidly rising trends of overweight/obesity cannot be overemphasized .