The cathode microporous layer (MPL), as one of the key components of the proton exchange membrane fuel cell (PEM-FC), requires specialized carbon materials to ensure the two-phase flow and interfacial effects. In this respect, we designed a novel MPL based on highly hydrophobic carbon nanowalls (CNW). Employing plasma-assisted chemical vapor deposition techniques directly on carbon paper, we produced high-quality microporous layers at a competitive yield-to-cost ratio with distinctive MPL properties: high porosity, good stability, considerable durability, high hydrophobicity, and substantial conductivity. The specific morphological and structural properties were determined by scanning electron microscopy, X-ray photoelectron spectroscopy, and Raman spectroscopy. Thermo-gravimetric analysis was employed to study the nanostructures’ thermal stability and contact angle measurements were performed on the CNW substrate to study the hydrophobic character. Platinum ink, serving as a fuel cell catalyst, was sprayed directly onto the MPLs and incorporated in the FC assembly by hot-pressing against a polymeric membrane to form the membrane-electrode assembly and gas diffusion layers. Single-fuel-cell testing, at moderate temperature and humidity, revealed improved power performance comparable to industrial quality membrane assemblies (500 mW cm−2 mg−1 of cathodic Pt load at 80 °C and 80% RH), with elevated working potential (0.99 V) and impeccable fuel crossover for a low-cost system.