Background Unacceptably high rate of childhood stunting for decades remained a puzzle in the eastern Indian state of Bihar. Despite various programmatic interventions, nearly half of the under-five children (numerically about 10 million) are still stunted in this resource-constrained state. Data and Methods Using four successive rounds of National Family Health Survey (NFHS) data spread over more than two decades and by employing quantile regressions and counterfactual decomposition (QR-CD), the present study aims to assess effects of various endowments as well as returns to those endowments in disparities in childhood stunting over the period. Results The results show that although child’s height-for-age Z-scores (HAZ) disparity was largely accounted for differing levels of endowments during earlier decade, in the later periods, inadequate access to the benefits from various development programmes was also found responsible for HAZ disparities. Moreover, effects of endowments and their returns vary across quantiles. We argue that apart from equalizing endowments, ensuring adequate access to different nutrition-centric programmes are essential to lessen the burden of childhood stunting. Conclusion The state must focus on intersectoral convergence of different schemes in the form of state nutrition mission, and, strengthen nutrition-centric policy processes and their political underpinnings to harness better dividend.