Compton scattering imaging with intense, high-energy synchrotron X-rays allows us to visualize a light element substance in an operating electrochemical device. In this paper, we report the first experiment of Compton scattering imaging (CSI) on an operating polymer electrolyte fuel cell (PEFC). The novelty of the CSI technique is a non-destructive direct observation of cross-sectional images with a sensitivity to light elements and a capability of simultaneous measurements with fluorescent X-rays of heavy elements. Analyses of the observed images provide the cross-sectional distribution of generated liquid water and its current density dependency. The results show that the amount of generated water increases in the vicinity of the cathode catalyst layer at current densities ranging from 100 to 500 mA/cm2, while it remains constant or slightly decreases from 500 to 900 mA/cm2. In both the gas diffusion layer and the channel, liquid water is observed near the channel and rib interface above 500 mA/cm2, indicating the formation of a liquid water flow path. In addition, simultaneous measurements of fluorescent Pt-Ka X-rays reveal a significant correlation between the generated liquid water and Pt catalysts, using the Pearson correlation coefficient. The result shows that water is dispersed in the catalyst layer without any correlation with the amount of Pt catalysts at low current densities, but water tends to be distributed in the Pt-rich areas at high current densities. This study demonstrates that Compton scattering imaging is one of the unique techniques to characterize the behavior of generated liquid water in an operating PEFC.