Salmonellosis is an important cause of morbidity in tropical regions.This study aims to describe the epidemiology of non-typhoidal Salmonellae (NTS) in children presenting to public hospitals in Queensland, Australia, over the past 20 years, with a focus on differences between tropical and sub-tropical zones in the region. This is a retrospective and descriptive cohort study of 8162 NTS positive samples collected in 0-17-year-olds from the Queensland public hospital pathology database (Auslab) over a 20-year period from 1997 to 2016. There were 2951 (36.2%) positive NTS samples collected in tropical zones and 5211 (63.8%) in the sub-tropical zones of Queensland, with a total of 8162 over the region. The tropical zone contributed a disproportionately higher number of positive NTS samples by population sub-analysis. Of the specimens collected, 7421 (90.92%) were faecal, 505 (6.2%) blood, 161 (1.97%) urine, 13 (0.16%) cerebrospinal fluid (CSF) and 62 of other origin. Other categories of specimen types isolated include swab, fluid, aspirate, lavage, bone, tissue, isolate and pus, and these were not included in sub-analysis. The most commonly identified serovars were Salmonella Typhimurium, Salmonella Virchow and Salmonella Saintpaul. This is the first and largest study that emphasises the high burden of invasive and non-invasive NTS infections resulting in hospital presentations in the paediatric population of tropical north Queensland, compared to the sub-tropics.