Microporous layers (MPLs) play a crucial role in improving water management in proton exchange membrane fuel cells (PEMFCs). Highly tunable electrospun carbon fibers offer a promising candidate for MPLs to facilitate two-phase water and gas transport in PEMFCs. In this work, we present a two-phase PEMFC model to investigate the mass transport characteristics with MPLs made of nano-/micro-fibers. Simulations were validated by the reported experimental results. It is revealed that the fiber-based MPLs (fMPLs) reduce the liquid water saturation at the cathode side due to the higher permeability, thus significantly reducing the oxygen transport resistance and resulting in superior cell performance than conventional MPLs (cMPLs) do. Moreover, PEMFCs with fMPLs outperform those with cMPLs under a wide range of operating temperatures from 40 to 80 °C. In addition, our parametric study results suggest that fMPLs with a high porosity (> 0.5), a large fiber diameter (> 2 µm), and a large contact angle (> 135°) can effectively boost water drainage and gas transport, thereby considerably enhancing the PEMFC performance. This work provides insights into the two-phase transport behavior in PEMFCs with fMPLs, paving the way for design and development of novel MPLs for high-performance PEMFCs.