The role of gender inequality in childhood immunization is an emerging area of focus for global efforts to improve immunization coverage and equity. Recent studies have examined the relationship between gender inequality and childhood immunization at national as well as individual levels; we hypothesize that the demonstrated relationship between greater gender equality and higher immunization coverage will also be evident when examining subnational-level data. We thus conducted an ecological analysis examining the association between the Subnational Gender Development Index (SGDI) and two measures of immunization—zero-dose diphtheria-tetanus-pertussis (DTP) prevalence and 3-dose DTP coverage. Using data from 2010–2019 across 702 subnational regions within 57 countries, we assessed these relationships using fractional logistic regression models, as well as a series of analyses to account for the nested geographies of subnational regions within countries. Subnational regions were dichotomized to higher gender inequality (top quintile of SGDI) and lower gender inequality (lower four quintiles of SGDI). In adjusted models, we find that subnational regions with higher gender inequality (favoring men) are expected to have 5.8 percentage points greater zero-dose prevalence than regions with lower inequality [16.4% (95% confidence interval (CI) 14.5–18.4%) in higher-inequality regions versus 10.6% (95% CI 9.5–11.7%) in lower-inequality regions], and 8.2 percentage points lower DTP3 immunization coverage [71.0% (95% CI 68.3–73.7%) in higher-inequality regions versus 79.2% (95% CI 77.7–80.7%) in lower-inequality regions]. In models accounting for country-level clustering of gender inequality, the magnitude and strength of associations are reduced somewhat, but remain statistically significant in the hypothesized direction. In conjunction with published work demonstrating meaningful associations between greater gender equality and better childhood immunization outcomes in individual- and country-level analyses, these findings lend further strength to calls for efforts towards greater gender equality to improve childhood immunization and child health outcomes broadly.