Microbial fuel cells (MFCs) are electrochemical convertors that can convert chemical energy of organic matters with catalytic microorganisms to electrical energy. One of the important factors for increasing the efficiency of the cell output is the optimal input flow rate. In this study , the effect of flow rate from the anode chamber in herbal medicine wastewater treatment and using of it as the organic matter to produce electricity was investigated in the MFC. This procedural system contained a dual-chamber MFC with Nafion membrane as a separator and equipped with an Fe@Fe2O3/graphite as catalysy in electrode. The dual chamber MFC with continuous flow was used for 2 months at ambient temperature and different flow rate of anolyte. With increasing input flow rate from 0.1 to 1.6 ml/min, power density and voltage input increased from 95.05 to 366.13 mW/m2 and 627 to 844 V, repectively, while the removal of COD decreased from 75% to 31%. Also, the maximum produced power was obtained in substrate degradation rate of 1.81 g COD/l.d and F:M 0.584 mg COD/mg MLSS.d. In addition, the changes of pH was lower in high flow rate due to low activity of microorganisms The results show that microbial fuel cell can be used as a cost-effective technology for herbal medicine wastewater treatment and production of electricity simultaneously