A polyimide substrate based microfluidic chip with thousands of comb-shaped microelectrodes has been designed, fabricated, and tested for sterilization of bacteria by using pulsed electric field. The performance of bacteria sterilization as functions of the electric field strength, pulse number and width, treatment buffer, bacteria growth status, and bacteria enrichment by positive dielectrophoresis has been experimentally investigated on the microfluidic chip. Experimental results show that only 100 V are sufficient to obtain good sterilization of Escherichia coli. Higher electric field strength, bacteria enrichment by positive dielectrophoresis, longer pulse time, buffer with fewer components and nutritions, and suitable bacteria growth status also improve the sterilization of bacteria. In addition, configuration of the microelectrode array affects bacteria sterilization. This microfluidic device allows one to preconcentrate bacteria to a region with high electric field strength by using positive dielectrophoresis, and subsequently kill the enriched bacteria by applying a pulsed electric field through the same microelectrode array.