Abstract Background The prevalence of otitis media (OM) and related hearing loss has remained persistently high among some groups of Australian Aboriginal children who are also reported to have poor academic outcomes. The general literature remains inconclusive about the association between OM-related hearing loss and academic performance in primary school. This study aimed to investigate this association in Aboriginal children living in the Northern Territory (NT) of Australia. Methods A retrospective, observational cohort study was conducted for 2208 NT Aboriginal children, aged about 8 years, living in remote and very remote communities. The explanatory variable was audiometrically determined hearing level as recorded in the Remote Hearing Assessment dataset. The outcome variable consisted of scale scores in the five domains of the National Assessment Program – Literacy and Numeracy (NAPLAN) for Year 3. Other linked datasets used in the study included school attendance records, perinatal records and community level information on relative remoteness, socioeconomic disadvantage and housing crowdedness. Fixed effects linear regression models were used for statistical analyses. Results Compared with children with normal hearing and after controlling for a range of covariates, children with mild hearing impairment (HI) scored lower in Writing and Spelling by 15.0 points (95% CI: − 22.4 to − 7.6, p 5 persons, living in a very remote community and speaking English as a second language. Conclusions OM-related HI was independently associated with poorer early year academic achievement in Aboriginal children living in remote NT communities. Interventions to improve academic outcomes for Aboriginal children must incorporate actions to address the negative impact associated with HI through early detection, effective treatment and ongoing support for affected children.