The facilitated transport of ethyl docosahexaenoate (DHA-Et) through the thin solution-cast perfluorosulfonated ionomer membranes has been studied. The carrier of DHA-Et was silver ion and was immobilized in the support ionomer membrane by electrostatic forces. In this system, the feed phase, membrane phase, and receiving phase had the same solvent. This system was already proved to be highly stable in our previous work. When ethanol/water (85/15) was used as the solvent, the DHA-Et permeance in the cast membrane was about four times higher than that in the commercial Nafion 117 membrane, due to the smaller membrane thickness. In the case of acetone solvent, a high selectivity of DHA-Et to ethyl oleate of 42 and a high facilitation factor of 153 were obtained. These membrane performances were superior to those of the Nafion 117 membrane. The effects of membrane preparation conditions, such as annealing temperature and kinds of polar solvents added to the ionomer solution before annealing, on the membrane performance was investigated in detail. Furthermore, small-angle X-ray scattering (SAXS) measurement was carried out to study the membrane structure. The experimental result suggests higher crystallinity in the cast membrane annealed at higher temperature.