Background In the tribal state of Jharkhand, there have been very few studies on micronutrient deficiency and how it is addressed among school children. This study was conceived and undertaken to assess the effect of milk supplementation on the micronutrient status of school children. Design A comparative observational study was conducted among school children of a tribal district in India during 2017–2018. Two groups of schools/clusters were randomly selected, one with milk supplementation and the other without supplementation. A total of 318 children from the two groups of schools were recruited for biochemical analysis of certain micronutrients, such as calcium, vitamin D, vitamin B12 and iron (haemoglobin level), using cluster random sampling. Data were analysed using SPSS V.20.0 software, and multiple logistic regression analysis was done to determine the predictors of serum calcium and vitamin B12 level among school children. Results Almost all children from both groups had vitamin D deficiency. A higher risk of lower serum vitamin B12 level (OR 2.59, 95% CI 1.61 to 4.16) and calcium level (OR 3.36, 95% CI 1.74 to 6.49) was observed in children of the control group. The difference in the proportion of anaemia in the two study groups was found to be statistically insignificant. Milk consumption was found to be the only significant predictor of normal vitamin B12 and calcium level in the present study. Conclusions In this study, it was concluded that milk consumption may help in improving the calcium and vitamin B12 status of school children of a tribal state, whereas it does not have any significant effect on vitamin D level.