Smoking is one of the oldest technologies for processing and preserving raw materials of animal origin. To this day, smoked fish is very popular among consumers. The most popular smoked fish is salmon. The research compared the qualitative changes in the fat fractions of hot and cold-smoked salmon during refrigerated storage. Generally accepted physicochemical methods for assessing the quality of fats, such as peroxide, anisidine, and acid number, were used. First, the smoked salmon was stored, and then, the samples were analyzed to find changes in the fatty acids EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid). It was shown that cold smoking significantly inhibited the increase in the level of lipid oxidation compared to hot smoking and raw samples stored in the same way. In the meat of stored and cold- and hot-smoked salmon, the TOTOX values remained at the level indicated by the Codex Alimentarius. Hot smoking limited the degree of lipid hydrolysis during storage as compared to cold smoking. The smoking process had a protective effect on EPA and DHA acids. In the raw samples, the loss of these acids was three times higher. Summarizing the research, it can be concluded that smoked products are a good and safe source of omega-3 fatty acids in the diet.