Two different kinds of nano-ZnO (nanoparticle and nanorod) were embedded in a PES membrane matrix to investigate the effects of a nanofiller shape on the antifouling capability of the nanocomposite membrane. The membranes were prepared by embedding 0.1 wt.% nano-ZnO into the polymer solution and precipitating during a phase inversion process. The effect of the nanofiller shape on the membrane characteristics and performance was investigated in terms of water contact angle measurement, scanning electron microscopy (SEM), atomic force microscopy (AFM) techniques, pure water flux and fouling resistance tests. The water contact angle measurements confirmed increment of hydrophilicity of nanocomposite membranes, particularly in the ZnO nanorod mixed membranes. Fouling resistance of the membranes probed by powder milk solution filtration revealed that ZnO nanorod membrane has the best antifouling property. PWF and antifouling characteristics of prepared nanocomposite membranes embedded with 0.1 wt.% of both types of ZnO nanofillers increased in comparison with pristine PES membrane; however, the best performance came from membrane prepared with ZnO nanorods.