This article describes long-term trends in hospital discharge rates and notifications for invasive bacterial infections caused by Streptococcus pneumoniae (IPD), Neisseria meningitidis and Haemophilus influenzae type B (Hib) in NZ children (aged <15 years), the impact of vaccines on the rates of these diseases and rates in comparison to UK data. Two datasets were used: the National Minimum Dataset for data on hospital discharges from all private and public hospitals in NZ and EpiSurv, NZ’s national database for notifiable disease surveillance. Hospitalisation rates for Hib fell by 84% within 2 years after the introduction of the vaccine (from 13.53/100,000 in 1993 to 2.19/100,000 in 1995). Hospitalisation and notification rates were similar for Hib. After the introduction of MeNZB vaccine in 2004, hospitalisation rates for meningococcal disease fell by 73% within 3 years: from 36.68 per 100,000 in 2003 to 10.05 per 100,000 in 2006. Over the 8 years after the introduction of MeNZB vaccine, notification rates for meningococcal disease declined by 75%, from 26.15 per 100,000 to 2.48 per 100,000 and continued to decline. From 2007 to 2011, the rates of meningococcal disease in NZ were lower than those in the UK (8.16 vs 10.37/100,000), despite NZ not having a meningococcal vaccine on the immunisation schedule for those years. NZ hospitalisation rates for IPD fell by 62% within 2 years of the introduction of PCV7 vaccine (from 7.80/100,000 in 2007 to 2.98/100,000 in 2009). Notification rates were 3–6-fold higher than the hospitalisation rates, but also fell markedly after the introduction of PCV7 vaccine. Rates of invasive bacterial disease have fallen substantially in NZ children since the introduction of meningococcal and pneumococcal vaccines, with the greatest absolute reductions in disease incidence amongst Māori children, although disparities are still apparent between Māori and non-Māori children.