(1) Background: The empowerment of women contributes to better child health and wellness. This study aimed to examine the association between women’s empowerment and complete vaccination of children, as recommended in the National Expanded Program on Immunization (EPI) in the Democratic Republic of the Congo (DRC). (2) Methods: In this cross-sectional study, a principal component analysis (PCA) was conducted on data from the Multiple-Indicator Cluster Survey 6 (MICS-6) to determine the dimensions of women’s empowerment. Logistic regression analysis was used to assess the association between women’s empowerment and complete vaccination of children stratified by household wealth. In total, 3524 women with children aged 12–23 months were included in the study. (3) Results: Women’s empowerment was defined by three dimensions, namely intrinsic agency, enabling resources, and social independence. Children of women with high levels of empowerment had higher odds of complete vaccination, with values of 1.63 (p = 0.002) and 1.59 (p = 0.012) for intrinsic agency and enabling resources of the empowerment, respectively, compared to the children of women with low levels of empowerment; however, social independence failed to be associated with the vaccination status of children. After stratification by household wealth, the OR of complete vaccination was higher in women from middle-income households with high levels of intrinsic agency (OR: 2.35, p = 0.021) compared to women from poor households with high levels of intrinsic agency (OR: 1.92, p = 0.004). (4) Conclusions: Higher levels of women’s empowerment, especially intrinsic agency and enabling resources, were associated with complete vaccination in children in the DRC. Household wealth status influenced the associations. The empowerment of women is crucial in promoting the complete vaccination of children and providing equal access to vaccines.