This study used a series of individual-level datasets from National Family Health Surveys conducted in 1998–99, 2005–06 and 2015–16 to assess the factors behind the reduction in childhood stunting and underweight in India between the years 1998–99 and 2015–16. A multivariable decomposition regression analysis was performed. Results showed that the prevalence of childhood stunting declined from 49.4% in 1998–99 to 34.9% in 2015–16. Over the same period, the prevalence of childhood underweight declined from 41.9% in 1998–99 to 33.1% in 2015–16. The reduction in the prevalence of stunting was found to be contributed largely by a reduction in the combined prevalence of stunting and underweight (60%), followed by stunted only (21%) and the combined prevalence of stunting, underweight and wasting (19%). Likewise, the reduction in the prevalence of underweight was contributed by a reduction in the combined prevalence of stunting and underweight and the combined prevalence of stunting, underweight and wasting. Results of the decomposition analysis showed that over the period 1998–99 to 2015–16, improvement in wealth status and maternal education led to 13% and 12% declines, respectively, in childhood stunting and to 31% and 19% declines, respectively, in childhood underweight. Furthermore, reductions in childhood stunting and underweight were due to an increased average number of antenatal care visits, lower average birth order, decreased share of children with below-average birth size, increased use of clean fuel for cooking and a reduction in the practice of open defecation. These findings suggest that further reduction in the prevalence of childhood stunting and underweight could be attained through more equitable household economic growth, investment in girl’s education, greater access to improved toilet facilities, more widespread use of clean fuel for cooking, reduction in average birth order, increased antenatal care visits and greater consumption of IFA tablets by pregnant women. Policymakers need to prioritize these measures to further reduce malnutrition among Indian children.