Children in many societies are found vulnerable to adverse socio-economic conditions, which usually undermine their growth and rob them of schooling opportunities. Without the availability of proper nutritional diet and full immunization, children suffer from underweight, stunted and wasted growth relative to their age. Poverty also weakens health and educational development of children. Principal Component Analysis has been applied to calculate a health related deprivation index for children. A recursive simultaneous equation framework has been used to explain the variation of health deprivation of children as well as educational deprivation across the major Indian states, on the basis of some identified explanatory variables. The health deprivation index’s empirical analysis reveals that factors such as poverty, female literacy rate, low body mass index of mother and full antenatal care, have significant association with the level of deprivation. The dropout rate of children is considered as reflective of their educational deprivation. Household characteristics of the deprived children indicate that female literacy, poverty, availability of electricity, gender of household’s head, fuel collection activity and children health status significantly influence the extent of their educational deprivation. This calls for urgent implementation of different government schemes for promoting better health and education of children of identified poor and deprived families.