For better water management in polymer electrolyte fuel cells (PEFCs), microporous layers (MPLs) are generally used. In this paper, hydrophilic MPLs having various pore volumes and diameters were prepared using a range of carbon materials, and the effect of the MPL on the membrane electrode assembly (MEA) performance was investigated under dry and wet conditions. Under the dry condition (80 • C, 30%RH), the MEA employing an MPL with a larger median pore diameter showed higher cell voltage, suggesting that the MPL with a larger pore diameter has better gas diffusivity, leading to better MEA performance. Under the wet condition (80 • C, 100%RH), it was confirmed that pore volume of the MPL has a significant impact on the MEA performance and that the hydrophilic MPL with a large pore volume was effective in reducing water flooding in the cathode catalyst layer. When used in an MPL, VGCF-H (carbon fiber with a fiber diameter of 150 nm) gives the largest pore diameter and pore volume. This MEA with a hydrophilic MPL (made of VGCF-H and ionomer) showed the best MEA performance under both dry and wet operating conditions.