Migrants and refugees generally experience immunization inequities compared to their host populations. Childhood vaccination coverage rates are influenced by a complex set of interrelated factors, including child and parental nativity. Coverage rates for MMR, pertussis, and HPV vaccines were compared among children born in Aotearoa New Zealand (NZ) of overseas-born parents or NZ-born parents. A nationwide retrospective cohort study was conducted using linked, de-identified data. Logistic regression models examined the most influential factors contributing to differences in timely vaccine uptake. Of the total study population who had received all scheduled vaccines (N = 760,269), 32.9% were children of migrant parents. Children of migrant parents had higher rates of complete and timely uptake for MMR, pertussis, and HPV vaccinations compared to non-migrant children. NZ-born children of migrant parents were significantly more likely to receive MMR and pertussis-containing vaccines on-time compared to those of non-migrants. All included factors, except for the child’s gender and parents’ English ability, significantly influenced vaccine uptake. Among NZ-born children of migrant parents, additional logistic modeling found significant differences based on parental duration of residence, visa group, and region of nationality. Findings point to the importance of differentiating between parent versus child nativity when examining immunization coverage. While vaccination rates were higher for NZ-born children of migrant parents, compared to non-migrant parents, timely coverage rates across both groups were below national targets. Continued efforts are needed to improve timely immunization service delivery to address suboptimal and inequitable coverage.