Given the surging economic and health costs associated with childhood stunting, identifying its associated factors is crucial. This study therefore explores a key determinant of long-term nutritional status, women’s participation in household decision-making in the context of Pakistan. To empirically estimate this association, three-level modelling was employed by pooling the data from two recent nationally representative survey rounds PDHS 2012–13 and PDHS 2017–18. Multilevel analysis was better suited compared to traditional methods for robust estimates because of the hierarchical nature of the data. Women’s decision-making power was measured by formulating an index through factor analysis from the direct questions about women’s participation in household decisions. This study found a positive association between women’s decision-making power and children’s nutritional growth at the national level, with no significant changes across the survey years. However, this relationship was moderated by regional variations, which was more pronounced in Sindh and relatively modest in other regions. The sensitivity analysis showed that among the different decision-making domains, only women’s participation in large household purchases was significantly and positively associated with child linear growth. The insights of this research suggest that nutrition-oriented policies should also consider non-nutritional factors, like women’s decision-making power when designing projects for target population. Meanwhile, it is also crucial to recognize that decision-making power is a contextual factor and its effect on child nutritional growth may vary across regions.