Although Arctic charr side streams contain limited amounts of fish flesh, they are a rich fish oil source (46.3 ± 0.6%). The aim of the study was to investigate the potential for valorization of Arctic charr filleting side streams through the extraction of oil by supercritical CO2 technology. The effect of temperature (40 °C and 80 °C) and pressure (20, 35 and 45 MPa) on the final extract after supercritical fluid extraction (SFE) was evaluated. Temperature increase enhanced the yield but decreased the antioxidant activity at 45 MPa, did not affect the yield and the antioxidant activity at 35 MPa, whereas yield was limited at 20 MPa and 80 °C. Extracts were rich in monounsaturated fatty acids (56.7–58.3%, especially oleic acid 37.2–38.0%), and polyunsaturated fatty acids (20.2–26.1%, especially DHA 7.3–11.4%). The presence of astaxanthin significantly preserved the extracts from oxidation. Industrial relevance: Supercritical carbon dioxide extraction is a green technology appropriate for the recovery of non-polar and heat sensitive compounds. The extracted Arctic charr oils were rich in polyunsaturated fatty acids and astaxanthin which inhibited oxidation in combination with the absence of oxygen and light during the process. This technology could be an excellent alternative for more sustainable valorization of fish processing side streams. © 2021 The Author(s)