This research concentrates on the comparison between anode methanol and cathode water liquid-phase polycyclic aromatic hydrocarbons (PAHs) emitted from a single direct methanol fuel cell (DMFC) at different operating parameters (methanol concentration, methanol flowrate, oxygen flowrate, and cell temperature). When the cell was operated at the standard test condition, the concentrations of PAHs in anode methanol and cathode water effluents were from non-detect (ND) to 0.143 ± 0.111 and ND to 0.155 ± 0.052 µg L–1, respectively; additionally, those of Total-PAHs were 0.343 ± 0.310 and 0.381 ± 0.093 µg L–1, respectively, while those of Total-BaPeq were 19.2 ± 19.6 and 160 ± 54 ng L–1, respectively. Naphthalene was almost the most dominant PAH species when changing one of the operating parameters. For the standard test condition, the anode and cathode emission factor (EF) sums of Total-PAHs and Total-BaPeq were 0.06 ± 0.03 µg g-electrode–1 and 15.7 ± 5.00 ng g-electrode–1, respectively. The EF sum of Total-PAHs (0.06 ± 0.03–3.41 ± 0.86 µg g-electrode–1) increased when increasing methanol flowrate or concentration and decreasing cell temperature, whereas that of Total-BaPeq (0.91 ± 0.52–33.2 ± 5.50 ng g-electrode–1) increased with increasing methanol flowrate or decreasing cell temperature and decreased with increasing methanol concentration or decreasing oxygen flowrate.