Abstract In this first of a series of two papers, we report an in-depth analysis of the impact of the gas diffusion layer (GDL) structure on the polymer electrolyte membrane (PEM) fuel cell performance through the use of custom GDLs fabricated in-house. Hydrophobic electrospun nanofibrous gas diffusion layers (eGDLs) are fabricated with controlled fibre diameter and alignment. The eGDLs are rendered hydrophobic through direct surface functionalization, and this molecular grafting is achieved in the absence of structural alteration. The fibre diameter, chemical composition, and electrical conductivity of the eGDL are characterized, and the impact of eGDL structure on fuel cell performance is analysed. We observe that the eGDL facilitates higher fuel cell power densities compared to a commercial GDL (Toray TGP-H-60) at highly humidified operating conditions. The ohmic resistance of the fuel cell is found to significantly increase with increasing inter-fiber distance. It is also observed that the addition of a hydrophobic treatment enhances membrane hydration, and fibres perpendicularly aligned to the channel direction may enhance the contact area between the catalyst layer and the GDL.