Gas diffusion layer (GDL) and its interfaces with the flow-channel and microporous layer or catalyst layer in polymer electrolyte fuel cells (PEFCs) play a significant role in water management and heat removal from the cells. Both surface morphology and surface wettability of GDL influence and control the water transport in PEFCs. Thus, the surface morphology and selectivity of its surface wettability are critical for PEFCs to provide optimum outputs. In this study, we have reported the fabrications of GDLs with a selective wetting pattern. Sigracet® GDLs were used as a substrate and two different monomers, polydimethylsiloxane (PDMS) added with fumed silica (Si) and fluorinated ethylene propylene (FEP), were used to print a selective pattern on the GDL surfaces. The evaluations of printed GDL surfaces, by means of static contact angle, sliding angles, and scanning electron microscopy image show that superhydrophobicity was achieved with both FEP and PDMS-Si coatings. Fourier transform infrared spectroscopy analysis confirmed the successful introduction of the functional groups in both the coatings. Finally, pore size distributions, sliding angle measurements, and adhesion forces were used to investigate the interactions between the water droplets and GDL surfaces. The results of this study demonstrate that the present approach provides a novel but simple way to tune GDL surfaces with selective wetting properties and obtain superhydrophobic interfaces. The electrochemical results showed that an improvement can be achieved for the performance of PEFCs with patterned GDL/flow-channel interfaces.