In this study, we develop a one-dimensional (1-D), two-phase, transient-thermal DMFC model to investigate the effect of methanol concentration fluctuation that usually occurs in active-type direct methanol fuel cell (DMFC) systems. 1-D transient simulations are conducted and time-dependent behaviors of DMFCs are analyzed under various DMFC operating conditions such as anode/cathode stoichiometry, cell temperature, and cathode inlet humidification. The simulation results indicate that the effect of methanol concentration fluctuation on DMFC performance can be mitigated by proper control of anode/cathode stoichiometry, providing a guideline to optimize operating conditions of active DMFC systems.