Background: Declining childhood immunisation represents a serious public health problem globally, and in New Zealand. To guide efforts to increase immunisation coverage, this study monitors nationwide change in immunisation coverage since the introduction of the National Immunisation Register (NIR) in 2005 and spatiotemporal patterns of immunisation coverage from 2006 to 2017. Methods: The study population consisted of 4,482,499 individual immunisation records that were obtained from the NIR (2005–2017). Data on yearly and average immunisation coverage in census area units (CAUs) in New Zealand were calculated by milestone age (6/8/12/18/24/60/144 months). Data for 2005 were excluded due to missing records in the introductory period of the NIR. We analysed spatial and spatiotemporal patterns using Gi* and SaTScan methods. Results: Immunisation coverage improved since the introduction of the NIR in 2005, reaching a peak in 2014 and 2015 with a slight decrease in 2016 and 2017. Well and insufficiently immunised areas were identified with spatial autocorrelation analyses highlighting several hot- and cold-spots. Comparison of CAUs with neighbouring CAUs allowed for the identification of places where immunisation coverage was significantly higher or lower than expected, over both time and space. Conclusion: We provide the first spatiotemporal analysis of childhood immunisation in New Zealand that utilises a large sample of over 4.4 million individual immunisation records. Our spatial analyses enable policymakers to understand the development of childhood immunisation coverage and make more effective prevention strategies in New Zealand.