Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) ethyl esters were effectively separated from oleic acid (OA) and palmitic acid (PA) ethyl esters by oil-in-water (O/W) emulsion liquid membranes containing silver nitrates as a mobile carrier. Since the silver ions in the liquid membrane phase have a high affinity to the carbon-carbon double bonds in polyunsaturated fatty acids (PUFA), DHA and EPA ethyl esters were selectively transported through the complex formation with the silver carrier from the internal material phase to the external recovery phase. The stability of the liquid membranes in the O/W emulsions was the most important factor to achieve a high recovery yield of their PUFA esters with a high purity. Surfactants were limited to nonionic surfactants to obtain a stable emulsion liquid membrane when containing the silver carrier. Concentrations of the surfactant and silver nitrates had a predominant effect to operate the PUFA separation by emulsion liquid membranes effectively. There is an optimal concentration for the silver nitrates and excess dosage of the carrier causes the instability of liquid membranes. Under the best conditions, 86% polyunsaturated fatty acid esters were successfully separated through the silver liquid membrane in a few minutes with a 98% purity.