Neutron radiography is a useful tool for the visualization of the water distribution in fuel cells. In this study, we prepared a high-spatial-resolution neutron imaging system and a small-sized fuel cell, and we observed the through-plane water distribution in the fuel cell after operation. Fuel cell operations were carried out while varying the gas flow rate in the constant-current mode. Under low-flow rate conditions, the voltage decreased as the operation time increased, dropping below 0.2 V after 7.5 min. A neutron image shows that water distribution was observed around the membrane electrode assembly (MEA) at the beginning of the operation, and it expanded over time to the gas diffusion layer (GDL) and the channel on the cathode side. The water thickness peak was located at the cathode-side GDL. Fuel cell operation was more stable under high-flow rate conditions than under low-flow rate conditions. Neutron imaging results suggest that stable fuel cell operation can be attributed to water discharge due to expulsion by the gas flow.