Product water transport via the microporous layer (MPL) and gas diffusion layer (GDL) substrate during polymer electrolyte fuel cell (PEFC) operation was directly and quantitatively observed by X-ray tomographic microscopy (XTM). The liquid water distribution in two types of MPLs with different pore size distributions (PSDs) was characterized as a function of the inlet gas relative humidity (RH) and current density under humid operating conditions at 45 °C. During the first minute of PEFC operation, liquid water mainly accumulated at the catalyst layer (CL)/MPL interface and in the GDL substrate close to the flow fields. Furthermore, under all tested conditions, saturation in the MPL was low (<25%), whereas under the rib, the saturation in the GDL was up to ca. 70%. Based on these XTM results, it is confirmed that in the high porosity MPLs, vapor transport was non-negligible even at high humidity conditions. Therefore, on top of the widely discussed MPL pore size and its distribution, it is proposed that the lower thermal conductivity from the high porosity of MPLs can also be a main cause of promoted vapor transport, reducing water saturation near the CL.