Long chain n‐3 polyunsaturated fatty acids from the refined oil from Sardinella longiceps were concentrated by low‐temperature crystallization and urea complexation. Low‐temperature crystallization (4°C) using acetone:ethylacetate (7:3, v/v) and urea complexation with urea‐to‐fatty acid ratio of 4:1 (w/w) afforded fatty acid concentrate (FAC) with greater than 60% C20–22 n‐3 fatty acids, and significant increase in NMR olefinic proton integral (at δ 5.2–5.6). Ethylacetate fractions of seaweeds, Kappaphycus alvarezii, Hypnea musciformis, and Jania rubens, which possessed greater antioxidant activities, were added to FAC individually, and in nine factorial combinations (0.5%, w/w). The oxidative stabilities of these treatments were compared with FAC added with BHT and α‐tocopherol in an accelerated storage study. A synergistic effect of ethylacetate fractions from K. alvarezii, H. musciformis, and J. rubens used at 0.1:0.2:0.2 (%, w/w) in preventing the oxidative degradation of FAC was observed. No traces of aromatics (δ 6–7) and aldehydes (δ 9–10) were present in the 1H‐NMR spectra of FAC added with seaweed extracts after the accelerated storage study, demonstrating that the seaweed extracts were able to prevent the formation of low molecular weight secondary oxidation products in the unsaturated system during storage.Practical applications: The present study demonstrated the process of concentrating the refined oil of S. longiceps using a step‐wise process of low‐temperature crystallization and urea complexation, which is significant to obtain greater than 60% C20–22 n‐3 fatty acids. The fatty acid concentrate has greater susceptibility towards oxidative rancidity resulting in the formation of toxic end products, and therefore, the prevention of oxidative deterioration of n‐3 fatty acid concentrates is a major challenge for the fish oil industry. Effectiveness of seaweed derived antioxidatives as natural alternatives to synthetic antioxidants to prevent the formation of oxidation products in the concentrated fatty acids from fish oil has been established. The utility of nuclear magnetic resonance analyses as an effective tool for analyzing the chemistry and stability of concentrated n‐3 polyunsaturated fatty acids has been demonstrated. This study is significant to produce stabilized fatty acid concentrate from marine fish oil for use in the food and pharmaceutical industries.Refined oil from Sardinella longiceps was concentrated by urea complexation to yield fatty acid concentrate (FAC) with greater than 60% C20–22 n‐3 fatty acids, and a significant increase in 1H‐NMR olefinic proton integral (δ 5.2–5.6). No traces of aromatics (δ 6–7) and aldehydes (δ 9–10) were present in 1H‐NMR of FAC added with seaweed extracts after accelerated storage, demonstrating that seaweed extracts could prevent the formation of low molecular weight secondary oxidation products in the unsaturated system during storage.