Polypyrrole films doped with p-toluenesulfonic anions on stainless steel mesh substrates were prepared by the electropolymerization method. A Zn/aqueous solution/polymer battery system was thus established with the polymer film as the cathode and three different biocompatible aqueous electrolytes. The mechanism of the anode reaction can be explained as the dissolution of Zn. It was found, however, that the discharge performance, including the discharge plateaus and capacities, were significantly affected by the polymer reactions. To elucidate the reaction mechanisms of the conductive polymer, its electrochemical properties were systematically studied by several techniques, including cyclic voltammetry, electrochemical impedance spectroscopy, and monitoring mass changes with an electrochemical quartz crystal microbalance. The redox states of polypyrrole before and after discharge were investigated by Raman spectroscopy. The reaction mechanisms of the polypyrrole film and its effects on the discharge performance are thus discussed based on the results.