Objective: Undernutrition is one of the leading causes of morbidity and mortality among under-five children, mostly affecting in the developing countries. Empowerment is an intrinsic agency developed in the affective domain. Since women, including mothers, are the primary caregivers of their children, so their empowerment status can influence children's nutritional status. This study aimed to assess the strength of association between women's empowerment and nutritional status of their children. Methods: Cross-sectional study was carried out among 300 mothers having children aged 6-59 month in rural municipalities of Kaski District, Nepal. Proportion to population size sampling technique was used to calculate the sample size and face to face interview technique was used to collect data. A Chi-square test was performed to assess the association between dependent and independent variables and multivariable logistic regression was used to assess the strength of association. Results: Of 300 mothers having 6-59 months’ children, nearly half (49%) were highly empowered but, overall, nearly two-fifth (37.7 %) children were in poor nutritional status. More than one-fourth (26.7%) children were stunted, 7% were wasted, 17.3% were underweight and 15% were acutely malnourished. There was a six-fold increase in odds of wasting, thirty-five-fold increase in odds of stunting, and thirty-six-fold increase in odds of underweight among children whose mothers had low empowerment status compared to their counterparts. Conclusion: Overall, this study exhibited that maternal empowerment strongly affects children’s nutritional status, especially wasting and underweight. Thus, intrinsic factor, like maternal empowerment, should be prioritized, in nutrition interventions of the under-five children.