Neutron imaging is a precise measurement tool for water content in proton exchange membrane fuel cells (PEMFCs), enabling the direct measurement of the water distribution in standard, commercially viable fuel cell hardware. In the last 5–7 years, neutron imaging has proven to be an invaluable tool in fuel cell research and has provided information inaccessible by any other measurement technique. The unique aspects of imaging real fuel cells are due to the large neutron scattering cross section from hydrogenous liquids, combined with the relatively small scattering cross section from many common metals and other materials of construction. Neutron‐imaging instruments are simple in design, and high‐resolution digital neutron‐imaging detectors (down to 20 µm) are routinely available at many neutron‐imaging facilities. One drawback of neutron imaging is that a high flux neutron beamline is required, and only 6–10 facilities in the world are currently equipped to do these types of measurements. The majority of this article discusses the uses of neutron imaging to investigate water transport phenomena in PEMFCs, including optimal channel design, effects of thermal gradients, and material property effects on liquid water retention. In addition, examples are given of neutron tomography applied to the study of other hydrogen‐based energy storage systems — metal hydride storage beds and alkaline batteries.