This paper reports a flow electroporation device, in which the Dean Vortex is employed to separate the cells from toxic by-product near the electrode during electroporation. This technique dramatically increases the cell viability, without decreasing the transfection rate. The flow-through chip can provide a continuous electroporation environment to expect to complete large doses of biological transfection requirement and allow high throughput. Furthermore, the simple structure of the proposed device eases the operation.