This study explores the association between childhood immunization and gender inequality at the national level. Data for the study include annual country-level estimates of immunization among children aged 12–23 months, indicators of gender inequality, and associated factors for up to 165 countries from 2010–2019. The study examined the association between gender inequality, as measured by the gender development index and the gender inequality index, and two key outcomes: prevalence of children who received no doses of the DTP vaccine (zero-dose children) and children who received the third dose of the DTP vaccine (DTP3 coverage). Unadjusted and adjusted fractional logit regression models were used to identify the association between immunization and gender inequality. Gender inequality, as measured by the Gender Development Index, was positively and significantly associated with the proportion of zero-dose children (high inequality AOR = 1.61, 95% CI: 1.13–2.30). Consistently, full DTP3 immunization was negatively and significantly associated with gender inequality (high inequality AOR = 0.63, 95% CI: 0.46–0.86). These associations were robust to the use of an alternative gender inequality measure (the Gender Inequality Index) and were consistent across a range of model specifications controlling for demographic, economic, education, and health-related factors. Gender inequality at the national level is predictive of childhood immunization coverage, highlighting that addressing gender barriers is imperative to achieve universal coverage in immunization and to ensure that no child is left behind in routine vaccination.