The industrial anthraquinone auto-oxidation process produces most of the world’s supply of hydrogen peroxide. For applications that require small amounts of H2O2 or have economically difficult transportation means, an alternate, on-site H2O2 production method is needed. Advanced drinking water purification technologies use neutral-pH H2O2 in combination with UV treatment to reach the desired water purity targets. To produce neutral H2O2 on-site and on-demand for drinking water purification, the electroreduction of oxygen at the cathode of a proton exchange membrane (PEM) fuel cell operated in either electrolysis (power consuming) or fuel cell (power generating) mode could be a possible solution. The work presented here focuses on the H2/O2 fuel cell mode to produce H2O2. The fuel cell reactor is operated with a continuous flow of carrier water through the cathode to remove the product H2O2. The impact of the cobalt–carbon composite cathode catalyst loading, Teflon content in the cathode gas diffusion layer, and cathode carrier water flowrate on the production of H2O2 are examined. H2O2 production rates of up to 200 μmol h−1 cmgeometric −2 are achieved using a continuous flow of carrier water operating at 30 % current efficiency. Operation times of more than 24 h have shown consistent H2O2 and power production, with no degradation of the cobalt catalyst.