Abstract Background India has an unacceptably high burden of vitamin A deficiency (VAD) among children aged 6–59 months. To mitigate VAD and its adverse effects on child health, the Indian government runs a nationwide vitamin A supplementation (VAS) programme. However, the effect of VAS in reducing child morbidity and mortality remains inconclusive and has been debated globally. In this paper, we estimate the effect of VAS on two indicators of child nutrition—anaemia (categorized into any anaemia, and mild/moderate anaemia) and anthropometric failure (categorized into stunting, wasting, and underweight) among children aged 6–59 months. Methods Using the nationally representative 2015–2016 National Family Health Survey data set from India, we set up a quasi-experimental study design and estimated household and mother fixed-effects of VAS on select types of child anaemia and anthropometric failure. Results Findings from both the household fixed-effects and mother fixed-effects analysis showed that VAS does not influence any types of childhood anaemia and anthropometric failure in India. We discussed the findings considering existing literature and possible limitations of the study. Conclusions The infirm effect of Vitamin A on anaemia and anthropometric failure is probably indicative of targeted VAS intervention, as opposed to a universal VAS programme. Impact Effects of vitamin A supplementation (VAS) in treating child morbidity and mortality remain inconclusive, which calls for further rigorous studies. This study set up a quasi-experimental research design and estimated the null effect of VAS on child anaemia and childhood anthropometric failure. While the cautious interpretation of findings is urged, this study reliably supports targeted intervention of VAS, instead of the universal VAS programme. The use of nationally representative data and robust research protocol are the primary strengths of this study.