Numerical analysis of cell membrane perforation in micro rectangular channels was performed to support the design of an on-chip droplet electroporation system. The computing software COMSOL Multiphysics 5.5 on Windows OS was used on the workstation HP Z8. The basic equations for the calculations were the current conservation equation and the asymptotic Smoluchowski equation for the calculation of cell membrane lysis, and the current conservation equation and the mobility equation were used for the calculation of electrophoresis. Under the above conditions, the numerical analysis by the finite element method was performed. When a cathode electrode and an anode electrode were arranged in the same plane, which is a low-cost electrode arrangement in a microreactor, it was found that two cell membrane lysis were formed at almost ideal positions.