Lower socioeconomic status has been linked to long-term stress, which can manifest in individuals as physiological stress. The aim was to explore the relationship between low socioeconomic status and physiological stress in Aboriginal and Torres Strait Islander Australians. Using data from the eGFR Study (a cross-sectional study of 634 Indigenous Australians in urban and remote areas of northern and central Australia), we examined associations between resting heart rate and demographic, socioeconomic, and biomedical factors. An elevated resting heart rate has been proposed as a measure of sustained stress activation and was used as a marker of physiological stress. Relationships were assessed between heart rate and the above variables using univariate and multiple regression analyses. We reported a mean resting heart rate of 74 beats/min in the cohort (mean age 45 years). On multiple regression analysis, higher heart rate was found to be independently associated with Aboriginal ethnicity, being a current smoker, having only primary level schooling, higher HbA1c and higher diastolic blood pressure (model R(2) 0.25). Elevated resting heart rate was associated with lower socioeconomic status and poorer health profile in Aboriginal and Torres Strait Islander Australians. Higher resting heart rate may be an indicator of stress and disadvantage in this population at high risk of chronic diseases.