Objective: To examine the association between childhood stunting and grade completion (as educational outcome) in South Africa. Design: Longitudinal study. Data was obtained using the National Income Dynamics Study over five waves (2008 to 2017). Children were tracked at wave 1 in 2008 until wave 5 in 2017 to determine their total years of schooling. We controlled for time-variant and time-varying confounding with a marginal structural model to estimate the associations between childhood stunting and subsequent grade completion. Setting: Nationally representative study of South African households. Participants: A total of 2629 children aged 2 and 3 in 2008. Results: We observed a substantial decrease in the prevalence of stunting between wave 1 (28.2%) and wave 4 (8.6%). Our marginal structural model results suggest that childhood stunting was significantly associated with decreased odds (22% less likely) of grade completion (OR = 0.78; 95% CI: 0.40, 0.86; p = 0.015), while those who were only stunted during early childhood had a 29% reduction in the odds of grade completion (OR = 0.71; 95% CI: 0.51, 0.82; p = 0.020). Conclusion: These findings underscore the fact that stunting is a significant predictor of academic achievement, whose effects might be long lasting.