Globally, diarrhoea is the third leading cause of death for under five-children. Women's empowerment can significantly reduce under-five mortality due to diarrhoea. This study investigated the association between women's empowerment and childhood diarrhoea in Benin using data from the 2017/18 Benin Demographic and Health Survey. A total of 7979 currently married women were included in the study. A logistic regression model was used to control for possible confounders. The prevalence of diarrhoea among children under five years of age was 13.6%. About 36.3% of the currently married women decided either alone or together with their husband on their own health, purchase of large household items and visiting family/relatives. Close to 65.4% of currently married women disagreed with all five reasons to justify wife-beating. The children of mothers who had decision-making power were less likely to have diarrhoea (aOR = 0.74, 95% CI: 0.57-0.96) than the children of mothers who had no decision-making power. Moreover, the children of mothers who disagreed with all five reasons to justify wife-beating (aOR = 0.79, 95% CI: 0.65-0.96) were less likely to have diarrhoea than the children of mothers who accepted wife-beating as a part of life. Women's age, educational level, wealth index and region were associated with childhood diarrhoea in Benin. The role of women's empowerment, as determined by decision-making power and wife-beating attitude, was found to be significantly associated with the risk of childhood diarrhoea in Benin, after adjusting for other variables. Therefore, it is essential for policymakers in Benin to reinforce strategies and interventions focusing on women's empowerment to avert childhood mortality caused by diarrhoea. This includes improving household economic status, women's education and decision-making power and enhancing awareness of women's human and democratic rights.