Porphyrin–fullerene composite systems are attracting great attention as photodynamic agents; however, water-soluble derivatives are still scarce. Herein, we prepared noncovalently a lipid membrane-incorporated porphyrin–fullerene composite system with relative stability in aqueous solution. As in the case of porphyrin–fullerene composite systems in nonpolar solvents, efficient formation of singlet oxygen occurred via photoinduced energy transfer between porphyrin and fullerene as the predominant pathway in the photodynamic activity under the hydrophobic conditions of the lipid membranes, resulting in enhanced photodynamic activity toward Colon26 and HeLa cells compared with the individual porphyrin and fullerene components. Furthermore, the porphyrin–fullerene composite system exhibited high selectivity toward HeLa cells over normal mouse fibroblast L929 cells.