We analysed socio-economic inequalities in stunting in South Asia and investigated disparities associated with factors at the individual, caregiver, and household levels (poor dietary diversity, low maternal education, and household poverty). We used time-series analysis of data from 55,459 children ages 6-23 months from Demographic and Health Surveys in Bangladesh, India, Nepal, and Pakistan (1991-2014). Logistic regression models, adjusted for age, sex, birth order, and place of residency, examined associations between stunting and multiple types of socio-economic disadvantage. All countries had high stunting rates. Bangladesh and Nepal recorded the largest reductions-2.9 and 4.1 percentage points per year, respectively-compared to 1.3 and 0.6 percentage points in India and Pakistan, respectively. Socio-economic adversity was associated with increased risk of stunting, regardless of disadvantage type. Poor children with inadequate diets and with poorly educated mothers experienced greater risk of stunting. Although stunting rates declined in the most deprived groups, socio-economic differences were largely preserved over time and in some cases worsened, namely, between wealth quintiles. The disproportionate burden of stunting experienced by the most disadvantaged children and the worsening inequalities between socio-economic groups are of concern in countries with substantial stunting burdens. Closing the gap between best and worst performing countries, and between most and least disadvantaged groups within countries, would yield substantial improvements in stunting rates in South Asia. To do so, greater attention needs to be paid to addressing the social, economic, and political drivers of stunting with targeted efforts towards the populations experiencing the greatest disadvantage and child growth faltering.