Background The increase in the frequency of extreme events due to climate change poses a serious challenge to achieving the Sustainable Development Goal 2 of ending hunger by 2030. While evidence exists on the impact of drought on under-five children, its effect during late childhood and early adolescence remains less investigated. Objective This study estimates the impact of concurrent and long-term exposure to drought on linear growth during late childhood and early adolescence. Methods Four rounds (2002–2013) of data from the young lives Cohort Study dataset (n = 2000) was used. The associations of concurrent and long-term exposure to drought and Height-for-age z-score was analysed using structural equation modelling techniques. The study also explored the mediating role of interim period growth in the association of early exposure to drought and undernutrition at later age and the role of the Productive Safety Net Program in buffering the impact of drought on child nutrition. Results Results show that both concurrent and long-term exposure to drought was negatively associated with Height-for-age z-score (p < 0.001). Exposure to drought at age 5, 8, and 12 years is associated with lower Height-for-age z- score at age 5, 8, and 12 years respectively. Exposure to drought at age 5 years was also negatively associated with Height-for-age z-score at age 12 years (p < 0.001). This association was mainly indirect (89%) and mediated through reduced child growth in subsequent years. Participation in productive safety net program by drought-affected children reduces but does not completely offset the negative effects of drought on Height-for-age z-score (p 0.7 was obtained [42]. All variables were standardized into dummy responses and a covariance matrix was used to obtain weights of principal components followed by Bartlett’s and KMO tests of homogeneity of variance across samples (p = 0.000 & KMO > 0.8) [43]. After computing the wealth index, households were classified into wealth tertile as low (1), medium (2), and high (3). Child age, sex, nutritional status of the child at round 1, child’s general health status, and dietary diversity were included as child level characteristics. Child age was measured in months and both linear and quadratic specifications were used to account for the non-linear growth of a child with age. Child sex was treated as a dichotomous variable that takes the value of “0” for a male and “1” for a female child. Among the household level covariates, maternal education was included as a categorical variable that takes a value of 0–4 if the mother had no, informal, primary, secondary, and higher education, respectively. The dependency ratio was computed as the number of non-working age members (0–12 years & >60 years) divided by the number of working age members (13–60 years) multiplied by 100. Participation in the PSNP was included as a dummy variable that takes the value of “1” if the household is a participant and “0” otherwise. With regard to community-level covariates, residence was included as a dichotomous variable that takes the value of “1” if the child lives in a rural locality and “0” otherwise. Access to a public health facility was also included as a dichotomous variable that takes the value of “1” if the child lives in a community where there is a public health facility and “0” otherwise. All analyses were done using Stata version 15 [39] and a probability level of 0.05 was used to consider results as significant. Children who were not present in two and more rounds of the survey (n = 327(5.45%)) and children with implausible values of HAZ (n = 5(0.08%)) were excluded from the analysis. For the rest of the sampled children, missing values were imputed using multiple imputations with chained equation and 20 replications in Stata. The imputed missing values include child age (n = 33), HAZ score (n = 83), DDS (n = 27), maternal education (n = 648), wealth index (n = 194), dependency ratio (n = 29), experience of drought (n = 28), PSNP participation (n = 23), child health (n = 28), and food insecurity (n = 4). No major difference in the sign and significance of coefficients was observed when comparing estimates of imputed and complete case analysis (results are available upon request). A structural equation model with the full information maximum likelihood (FEML) estimation approach was done using the ‘sem’ command in Stata 15. The overall fit of the models was assessed by the comparative fit index (CFI), Root Mean Squared Error of Approximation (RMSEA) and Standard Root Mean residual (SRMR). The parsimony index of the model was also assessed using Akaike’s information criterion (AIC)[44, 45]. Moreover, the total, direct, and indirect effects of drought on linear growth was also assessed. For robustness check, the data was fitted into ordinary least square regression, instrumental variable regression on the pooled and panel data structures, and child fixed effects. No major difference was found in the sign and significance of coefficients except a slight change in the magnitude of coefficients (S1 Table).