Nitrate ion, a pollutant and carcinogen in water, has been removed successfully in a microbial fuel cell with simultaneous generation of electricity in a lab scale. We used a system including two anode and cathode chamber to remove nitrate in the cathode chamber with generating energy by transferring electrons through an electrical circuit in ambient temperature. A voltage of 151 mV with an external resistance of 1000Ω observed where the maximum power density achieved was 1.375mW/m² with an external resistance of 800Ω. Seven days after the cell and without the presence of a catalyst, the amount of COD decreased by 25 percent. In addition, amount of nitrate decreased from 50 mg/L to 43mg/L. During 28 days of, daily removal of COD was 13 mg/L, and after this period of cell a significant decreasing of 78 percent was obtained for COD. Columbic efficiency of the process was reported to be 40 percent during 28 days that reflects the effectiveness of the system. In the presence of hexacyano ferrate as an excellent oxidant in the cathode the generated voltage were 4.5 times higher than when nitrate was used. This shows that nitrate can be successfully removed from water and wastewater treatment units with significant decrease in COD and generating electricity.