Economical Fe-N-C catalysts are considered as promising alternatives to platinum group metal catalysts for proton exchange membrane fuel cells (PEMFCs). Despite exhibiting robust activity on rotating disk electrodes, their performance within membrane electrode assemblies often experiences limitations, such as decreased O₂ diffusion, high H₂O₂ formation, low proton conduction, and a lower electron transfer number. In this study, key factors, including proton transport, electron conduction, and gas diffusion within air-breathing PEMFCs, have been investigated by adjusting cathode catalyst layer (CCL) compositions. From the experimental results, the optimal peak power density was obtained when the loading of Fe-N-C catalyst was 1 mg∙cm^–2 and Nafion content was 0.15 mg∙cm^–2 within CCLs. The addition of polytetrafluoroethylene to enhance hydrophobicity was found to have a negative impact on PEMFC performance. Furthermore, the incorporation of diverse carbon nanotubes into CCLs resulted in a significant increase of over 30% in peak power density, attributed to enhancements in the gas diffusion and proton conductivity. The critical roles of gas transport and proton conductivity within Fe-N-C-based CCLs have been highlighted by this study. These findings contribute to the advancement of rational design principles for economical PEMFCs, offering valuable insights to drive the development of efficient and cost-effective technology in future.