Background Racism is increasingly recognised internationally as a key factor contributing to health disparities. A comprehensive body of strong research from international authors has reported negative associations between racism and health outcomes. In Australia, although the literature is more limited, available findings follow global trends. Australia has an identified health gap between Aboriginal and Torres Strait Islander peoples and non-Indigenous Australians, and despite efforts to bridge this gap, health inequities continue to exist. This scoping review aims to assess, analyse and synthesise the relationship between racism and discrimination on the physical and mental health of Aboriginal and Torres Strait Islander peoples living in Australia.Method This is the study protocol for a scoping review. A systematic search will be conducted using five electronic databases: PubMed, CINAHL, Embase, Web of Science and the Australia’s National Institute for Aboriginal and Torres Strait Islander Health Research. The database search will include studies published between 2000 and 2020. Reference lists of the included articles will be searched. Outcome measures will include physical and mental health components including chronic conditions, depression and anxiety, psychological distress, social and emotional difficulties, suicide and health-related outcomes such as wellbeing and life satisfaction. Duplications will be removed, and titles and abstracts will be reviewed to select studies. Full-text screening of preselected studies will be performed by four reviewers independently, to select studies according to inclusion criteria. Included studies will be appraised for quality using appropriate tools tailored for each study design. Data will be extracted, and study findings and characteristics synthesised in a narrative summary. Discussion Our scoping review will synthesise the evidence on the impacts of racism and discrimination in relation to the physical and mental health of Aboriginal and Torres Strait Islander peoples living in Australia. These findings could guide future health interventions by addressing the exposure of racism and racial discrimination in order to reduce health disparity. It is anticipated the findings to be of interest to policymakers, researchers, Aboriginal and Torres Strait Islander communities and community health organisations and other stakeholders interested in optimising public health interventions for and in partnership with Aboriginal and Strait Torres Islander communities of Australia. Scoping review registration The protocol for this review has been registered on the International prospective register of systematic reviews (PROSPERO). The registration ID is CRD42020186193.