Indigenous Australians have poorer health outcomes compared to the non-Indigenous population. Malnutrition, and subsequently iron-deficiency anaemia, impairs childhood development. The aim of this study was to identify the prevalence of anaemia in school-aged children of an Australian Indigenous community and evaluate the effectiveness of treatment. A retrospective cohort study. A Northern Territory Indigenous community. Two hundred and one school-age students (5-15 years old) undergoing annual school screening. Presence of anaemia. Anaemic and non-anaemic students were compared to determine any differences in age, gender, BMI and past history of anaemia. The response to treatment was analysed using initial and repeat haemoglobin results. Altogether, 201 students were screened with 105 (52%) classified as anaemic. No significant association was found between anaemic students and age, gender, BMI or prior history of anaemia. After treatment, the mean rise in haemoglobin was 13% (95% CI 11-15) at the 4-week interval. Age (P = 0.17), gender (P = 0.53) and weight (P = 0.14) were not significantly associated with treatment efficacy. Only 11 students (17%) were still anaemic after treatment. Anaemia in Indigenous Australian school-aged children is a major public health issue. The prevalence of anaemia in this population is 52% and many times higher than that of the general Australian population. As per current guidelines, the recommended treatment is effective in over 80% at the 4-week interval. Community wide interventions are required to combat this alarming issue.