Migrants may experience a higher burden of vaccine-preventable disease (VPD)-associated hospitalisations compared to the host population. A retrospective cohort study from 2006 to 2015 was conducted that linked de-identified data from government sources using Statistic NZ’s Integrated Data Infrastructure. VPD-related hospitalisations were compared between three cohorts of children from birth to 5 years old: foreign-born children who migrated to NZ, children born in NZ of recent migrant mothers, and a comparator group of children born in NZ without a recent migration background. VPD-related hospitalisation rates were higher among NZ-born non-migrant children compared to NZ-born migrant and foreign-born children for all of the diseases of interest. For instance, 5.21% of NZ-born non-migrant children were hospitalised at least once due to all-cause gastroenteritis compared to 4.47% of NZ-born migrant children and only 1.13% of foreign-born migrant children. The overall hospitalisation rate for NZ-born non-migrant children was 3495 hospitalisations per 100,000 person years. Among children with migrant backgrounds, higher hospitalisation rates were noted among those of Pacific ethnicity and those with refugee backgrounds. Those arriving on Pacific visa schemes were hospitalised at rates ranging from 2644/100,000 person years among foreign-born migrant children and 4839/100,000 person years among NZ-born migrant children. Foreign-born quota refugee children and NZ-born children of quota refugee mothers were hospitalised at a rate of 4000–5000/100,000 person years. It is important to disaggregate migrant data to improve our understanding of migrant health. Children need to be age-appropriately vaccinated, and other individual and environmental factors addressed, to reduce the risk of infectious diseases.