BACKGROUND Marine‐derived omega‐3 polyunsaturated fatty acids (PUFA) are used globally as food supplements for their anti‐inflammatory properties and to reduce the risk of obesity, cardiovascular diseases, and cancer. New Zealand green‐lipped mussels (Perna canaliculus) contain diverse valuable compounds, including omega‐3 PUFA. The most abundant omega‐3 PUFA in Perna canaliculus are eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), both of which account for many of the health benefits accredited to these mussels. This research investigates the feasibility of using deep eutectic solvents (DESs) to isolate EPA and DHA from Perna canaliculus. RESULTS Twenty‐two hydrophobic DESs were screened using COSMO‐RS software to predict their affinity for EPA and DHA. Nine top‐ranked DESs were used for experimental extraction validation. The results exposed that the extraction capacity of the menthol: lidocaine DES (1:1 M ratio) for EPA and DHA was superior (172.04 μg EPA g−1 dry weight (DW) of biomass and 602.79 μg DHA g−1 DW) amongst other DESs. This was a considerably higher extraction yield than that observed using ethanol (95.65 μg EPA g−1 DW and 311.49 μg DHA g−1 DW). The optimisation of the menthol: lidocaine ratio identified a 1:2 M ratio as the optimal composition for this DES. The highest yields of EPA (267.59 μg g−1 DW) and DHA (1014.84 μg g−1 DW) were obtained by this optimised DES ratio at optimum extraction conditions (extraction temperature 65 °C, extraction time 2.12 h, and biomass loading 5 w/v%). The EPA and DHA showed good stability in the menthol: lidocaine DES over 7 days. This DES also showed good reusability, with a comparable extraction efficiency being observed after five extraction cycles. CONCLUSION This research revealed that menthol‐based DES can be a potential green solvent for the extraction of EPA and DHA from New Zealand green‐lipped mussels and it may be applicable for extracting other bioactive compounds with similar characteristics. © 2023 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).