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The kinetic parameters of ferrous iron oxidation, covering both lag and growth phases at low pH, were determined using a free suspended culture of the bacterium Leptospirillum ferriphilum. A mathematical model was developed to simulate the dynamics of a continuous bioreactor used for operation of a novel hybrid Fe(II)/Fe(III) redox flow fuel cell system. By changing the current load within a predefined range, three runs were performed to predict time-varying ferrous iron concentration, bacterial cell concentration, and pH as the major output variables of simulation program. The model was experimentally validated through three runs. It was found out that the key variable in dynamic analysis of the bioreactor was the current load applied. To optimize the bioreactor and the fuel cell conditions for a normalsteady-state operation, the optimal current profile for a transient phase was determined. A selected optimal policy was also implemented and validated during the mini-pilot-scale system experiments.