To reduce weight gain and encourage healthy eating including reduced sugar intake, Under 5 Energize (U5E) was introduced to 121 early-childhood-centres in the Waikato region of New Zealand in July 2013. Using anonymized data collected from January 2013 to September 2016 through free physical assessments of all 4-year-olds provided by the NZ Ministry of Health, the prevalence of obesity and dental decay children measured in the Waikato region was examined. Data were divided into four periods representing pre-implementation and 3 years of gradual implementation. Obesity was defined according to International Obesity Task Force criteria. Of 18,774 Waikato children included in the analysis, 32% were indigenous Māori, and 32% attended an U5E centre. Pre-implementation prevalences of obesity (4%) and visible dental decay (11%) of children attending and not-attending U5E centres were not different. While obesity prevalence did not change significantly over time, prevalence of dental decay decreased among children at U5E (trend p = 0.003) but not non-U5E (trend p = 0.14) centres, such that prevalences were significantly different between children at U5E vs. non-U5E centres at Year 3 (p = 0.02). The U5E intervention is a small but arguably effective part of the wider system approach that is required to improve children’s future health.