Background & Aims: Reports of a rise in childhood cancer incidence in Australia and globally prompted the investigation of cancer incidence and survival in South Australia (SA) and the Northern Territory (NT) over a 28-year period, with emphasis on Indigenous peoples. Methods: This cross-sectional analysis of two prospective longitudinal databases, the SA and NT Cancer Registries (1990–2017), included all reported cases of childhood cancers. Poisson regression provided estimates of incidence rate ratios and survival was modelled using Cox proportional hazard models for children aged <5 and ≥5 years. Results: A total of 895 patients across SA (N = 753) and the NT (N = 142) were ascertained. Overall and in the NT, childhood cancer incidence was higher in males compared with females (IRR 1.19 [1.04–1.35] and 1.43 [1.02–2.01], respectively). Lymphocytic leukemia was the most reported cancer type across all locations. With reference to the 1990–1999 era (181.67/100,000), cancer incidence remained unchanged across subsequent eras in the combined cohort (SA and NT) (2000–2009: 190.55/100,000; 1.06 [0.91–1.25]; 2010–2017: 210.00/100,000; 1.15 [0.98–1.35]); similar outcomes were reflected in SA and NT cohorts. Cancer incidence amongst non-Indigenous children significantly decreased from the 1990–1999 era (278.32/100,000) to the 2000–2009 era (162.92/100,000; 0.58 [0.35–0.97]). Amongst 39 Indigenous children in the NT, incidence rates remained unchanged across eras (p > 0.05). With reference to the 1990–1999 era, overall survival improved in subsequent eras in SA (2000–2009: HR 0.53 [0.38–0.73]; 2010–2017: 0.44 [0.28–0.68]); however, remained unchanged in the NT (2000–2009: 0.78 [0.40–1.51]; 2010–2017: 0.50 [0.24–1.05]). In the NT, overall survival of Indigenous patients was significantly lower compared with the non-Indigenous cohort (3.42 [1.92–6.10]). While the survival of Indigenous children with cancer significantly improved in the last two eras (p < 0.05), compared to the 1990–1999 era, no change was noted amongst non-Indigenous children in the NT (p > 0.05). Conclusions: The incidence of childhood cancers has remained unchanged over 28-years in SA and the NT. Encouragingly, improved survival rates over time were observed in SA and amongst Indigenous children of the NT. Nevertheless, survival rates in Indigenous children remain lower than non-Indigenous children.