The prime objective of the current investigation is to evaluate a promising alternative method for disinfection wastewater using a novel electro-oxidation unit. The study focused on determining the best-operating conditions from a techno-economic point of view to be applied to continuous flow simulating actual disinfection modules. The treatment unit consisted of a Plexiglas container with a 3 L volume containing nine cylindrical shape electrodes (6 graphite as anode and 3 stainless steel as a cathode) connected to a variable DC power supply. Determination of the best operating parameters was investigated in batch mode on synthetic wastewater by studying the effect of contact time, current density (CD), total dissolved solids concentration (TDS), and bacterial density. Moreover, the continuous mode experiment was considered on real wastewater from an agricultural drain and the secondary wastewater treatment plant effluent before chlorination. The batch mode results revealed that the best applicable operational conditions that achieved the complete removal of E. coli were at a contact time of less than 5 min, TDS of 2000 mg/L, and CD of 4 mA/cm2. Application of these conditions on the continuous mode experiment indicated the complete removal of all bacterial indicators after 5 min in the drainage wastewater and after 3 min in the secondary treated wastewater. Physico-chemical characterization also suggested that no chlorine by-products displaying the hydroxide ion formed due to water electrolysis is the main reason for prohibiting the growth of pathogenic microbes. The electrical consumption was calculated in the continuous mode and found to be 0.5 kWh/m3 with an operational cost of about 0.06 $/m3, including the cost of adding chemicals to increase the TDS. The results proved that this novel electro-oxidation unit is a robust and affordable disinfection method for complete bacterial removal from wastewater and is more environmentally benign than other conventional disinfection methods.