Undernutrition, particularly among children, is a crucial public health concern with significant disparities across different social groups. There is widespread economic and social inequality, as well as health and nutritional inequality. However, despite many flagships programs in India, particular to aspirational districts, schedule caste (SC) and schedule tribe (ST), are more susceptible to undernutrition among under-5 children. Furthermore, it may pose an obstacle to achieving Sustainable Development Goals (SDGs). Therefore, this study analysis the trends and patterns of undernutrition among under-5 children across different social groups in aspirational districts in India, and examine the association between child undernutrition with various level of covariate factors. We used data from the National Family Health Survey (NFHS) conducted in 2015–16 and 2019–21. NFHS-5 data have been used for the core analysis. Multiple logistic regression models were used to evaluate the association between various characteristics at the child, mother, and household levels and undernutrition in the different social categories among 112 aspirational districts in India. Comparing the nationwide prevalence of undernutrition to NFHS-4 and NFHS-5 across all socioeconomic classes, overall, the prevalence has declined. Whereas in NFHS-5 aspirational districts experienced an increase in the prevalence of undernutrition compared to non-aspirational districts. The important predictors of undernutrition were the birth order of the child, the mother’s level of education, the mother’s age at childbirth, and wealth quintiles. Additionally, the relationship between the sex of the child, place of residence and the factors such as water, sanitation, and hygiene practices was not consistent. However, we could not find statistical significance between the use of unimproved sanitation facility and a child’s undernutrition. The prevalence of undernutrition among aspirational districts was alarming. Therefore, this study suggests that policymakers should adopt community-based initiatives and more targeted inclusive policies at the regional level. These measures can effectively enhance marginalized children’s health and nutrition while promoting equity to advance the SDG Goals.