This study focuses on the comparison between gas- and water-phase polycyclic aromatic hydrocarbons (PAHs) emitted from a single hydrogen–oxygen proton exchange membrane (PEM) fuel cell (FC) at different flowrates and temperatures. The results show that among 21 PAHs, the most and least dominant species were Nap and BeP, respectively. At 65°C, the concentrations of individual gas- and water-phase PAHs decreased with increasing flowrate, and the PAH concentrations were lower at the anode than those at the cathode. The concentrations of gas-phase Total-PAHs and Total-BaPeq were slightly lower at 65°C than those at 90°C, but an opposite trend was observed for water-phase ones. The temperature influenced water-phase PAH concentration profiles more than gas-phase ones, and the gas- and water-phase PAHs had different concentration profiles. The performance of membrane-electrode assembly (MEA) decreased with increasing flowrate or temperature. The emission factor (EF) sum (anode + cathode) for gas- or water-phase Total-PAHs increased with increasing flowrate. This tendency was also true for gas-phase Total-PAHs EFs but not for water-phase ones when raising the temperature from 65°C to 90°C. At 65°C and 52/35 sccm, the EF sums of water-phase Total-PAHs and Total-BaPeq were 2.18 ± 0.04 and 0.09 ± 0.00 µg g-MEA–1, respectively—smaller than those of gas-phase ones (3.02 ± 0.09 and 0.12 ± 0.00 µg g-MEA–1, respectively). More environmental concern should be directed at emitted gas-phase PAHs than at water-phase ones because the anode and cathode water effluents are usually recycled during PEMFC operations.