The health gap between Indigenous and non-Indigenous Australians may be exacerbated by climate change if temperature extremes have disproportionate adverse effects on Indigenous people. To explore this issue, we analysed the effect of temperature extremes on hospital admissions for respiratory diseases, stratified by age, Indigenous status and sex, for people living in two different climates zones in the Northern Territory during the period 1993–2011. We examined admissions for both acute and chronic respiratory diagnoses, controlling for day of the week and seasonality variables. Our analysis showed that: (1) overall, Indigenous hospital admission rates far exceeded non-Indigenous admission rates for acute and chronic diagnoses, and Top End climate zone admission rates exceeded Central Australia climate zone admission rates; (2) extreme cold and hot temperatures were associated with inconsistent changes in admission rates for acute respiratory disease in Indigenous and non-Indigenous children and older adults; and (3) no response to cold or hot temperature extremes was found for chronic respiratory diagnoses. These findings support our two hypotheses, that extreme hot and cold temperatures have a different effect on hospitalisations for respiratory disease between Indigenous and non-Indigenous people, and that these health risks vary between the different climate zones. We did not, however, find that there were differing responses to temperature extremes in the two populations, suggesting that any increased vulnerability to climate change in the Indigenous population of the Northern Territory arises from an increased underlying risk to respiratory disease and an already greater existing health burden.