Brown shrimp, Crangon crangon (L.), is the most valuable target of coastal fisheries in the southern North Sea. Annual landings exceeded 30,000 tons in the last decade, yielding up to 100 Mio Euro. The shrimp are boiled immediately after capture onboard the fishing vessel for preservation and easy peeling. After landing, the shrimp are collected by traders and exported for manual peeling. Only the muscle of the pleon is returned and sold as regional delicacy. The remains, comprising the cephalothorax, the shell of the pleon, and, in case, adhering eggs, account for up to 70% of the total body mass. This potential resource, for example as aquaculture feed, has not yet been considered for exploitation. In this respect, the fatty acid (FA) profile and the share of essential FAs are crucial quality factors. Since boiling alters the quality of shrimp, this study evaluates changes in the FA composition of shrimp muscle and remains by comparing frozen and boiled samples. Major FAs in C. crangon were the saturated palmitic acid (PA, 16:0), accounting for 16.6%–19.1% of total fatty acids (TFAs), and the long-chain polyunsaturated FAs (LC-PUFAs) eicosapentaenoic acid (EPA, 20:5(n-3), 16.1–21.6%TFA ) and docosahexaenoic acid (DHA, 22:6(n-3), 11.5–13.6%TFA ). Frozen muscle and frozen remains showed similar FA profiles. Boiling changed the FA profile. PA, EPA, and DHA decreased by up to 25%, whereas palmitoleic acid 16:1(n-7) and oleic acid 18:1(n-9) increased by 2% to 3% each. Boiled muscle and boiled remains showed similar FA profiles. Despite the loss of FAs, the boiled shrimp remains are suggested to be a suitable PUFA supplement for aquaculture feeds, deserving further investigation.