Two different kinds of nano-ZnO (nanoparticle and nanorod) were synthesized, characterized, and embedded in a PES membrane matrix to investigate the effects of a nanofiller shape on the mixed matrix membrane characteristics and the antifouling capability. The mixed matrix membranes were fabricated by mixing different amounts of nanofillers with dope solution followed by a phase inversion precipitation technique. The effect of the shape of the embedded nanofillers on the morphology and performance of the fabricated membranes was studied in terms of pure water flux, fouling resistance, hydrophilicity, surface, and bulk morphology by means of permeation tests, milk powder solution filtration, water contact angle and porosity measurements, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques. Water flux of the mixed matrix membranes significantly improved after the addition of both types of ZnO nanofillers due to a higher hydrophilicity and porosity of the prepared membranes. The water contact angle measurements confirmed the increased hydrophilicity of the modified membranes, particularly in the ZnO nanorod mixed membranes. Fouling resistance of the membranes assessed by powder milk solution filtration revealed that 0.1 wt% ZnO nanorod membrane has the best antifouling property. The prepared mixed matrix membranes embedded with 0.1 wt% of both types of ZnO nanofillers showed a remarkable durability and reusability during the filtration tests; however, the best performance came from membrane prepared with ZnO nanorods.