Seafood products are a crucial dietary source of n-3 polyunsaturated fatty acids (n-3 PUFA), which are essential for human health. However, the presence of these n-3 PUFA may be subject to changes related to different processing methods. The aim of this study was to determine the fatty acid composition, focusing on n-3 PUFA, in different processed fish and shellfish products of both EU and non-EU origin. The products were purchased from supermarkets and ethnic food shops in Messina (Italy). Gas chromatography with a flame-ionization detector (GC-FID) was used for analysis. Based on the fatty acid profile, the atherogenicity index (AI), thrombogenicity index (TI), and flesh lipid quality index (FLQ) were determined: 0.13–1.04 (AI), 0.19–0.89 (TI), and 0.41–29.90 (FLQ). The percentages of saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids fell within the following ranges: 13.55–50.48%, 18.91–65.58%, and 13.84–52.73%, respectively. Considering that all samples showed low AI and TI indices and that all processed fish products proved to be a good source of beneficial PUFAs, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), their consumption is recommended for humans.