Aim: To describe the epidemiology of invasive Salmonella disease in children in the Northern Territory, Australia. Methods: Design: A retrospective review of invasive salmonellosis cases identified by pathology records and the Northern Territory Notifiable Disease Surveillance System. Case definitions: Those aged 18 years or under, with Salmonella cultured from a usually sterile site, collected in the Northern Territory between 1 July 2005 and 30 June 2015. Outcome measures: The primary outcome measure was the annual incidence rate of invasive salmonellosis, comparing rates between Indigenous and non-Indigenous children. Results: There were 86 cases of invasive Salmonella infection in children over the 10-year period; an annual incidence of 14.1 per 100 000 population, in those aged less than 18 years. Gastrointestinal Salmonella notifications were similar between Indigenous and non-Indigenous children. In children aged less than 15 years, the rate of invasive salmonellosis was higher in Indigenous children compared to non-Indigenous children (23.4 per 100 000 compared with 11.6 per 100 000); rate ratio 2.0 (95% confidence interval 1.3–3.3, P = 0.002). Indigenous children with invasive salmonellosis had a median hospital stay of 8 days, which was compared to 5 days for non-Indigenous children (P = 0.015). The highest incidence rate of invasive salmonellosis occurred in Indigenous patients less than 12 months of age (138 per 100 000). Conclusion: The Northern Territory of Australia has high rates of invasive salmonellosis in children. Indigenous and non-Indigenous children experience similar rates of Salmonella gastroenteritis but Indigenous children experience higher rates of invasive salmonellosis.