Climatic warming is most pronounced in the polar regions. For marine ectotherms such as fish, temperature is a key abiotic factor, influencing metabolic processes. Species distribution and abundance are driven by reproduction and growth, which depend on available energy exceeding baseline maintenance costs. These routine metabolic costs make up a large part of the energy expenditure. Thermal stress can increase routine metabolism, affecting an organism’s fitness. Data of routine metabolic rates of Antarctic fish are scarce, and comparability of existing data sets is often problematic due to ecological differences between species and in experimental protocols. Our objective was to compare routine metabolism and thermal sensitivity of species with similar ecotypes but different thermal environments to assess possible ecological implications of warming waters on energy expenditure in Antarctic fish, a fauna characterised by geographic isolation, endemism and putative thermal adaptation. We measured routine metabolic rates of three benthic Antarctic fish species from low- and high-Antarctic regions at habitat temperature and during acute temperature increase. Our analysis revealed differences in metabolic rates at the same temperature suggesting local adaptation to habitat temperature. Acute thermal stress induced a comparable response of metabolic rates to increasing temperature. We conclude that higher metabolic rates and thus higher energetic costs could be associated with narrower thermal windows, a potential disadvantage to the endemic high-Antarctic fish fauna facing the challenge of climate change.