Microfluidic channels with embedded micro-electrodes are of growing use in devices that aim to electroporate single cells. In this article we present an analysis of pore evolution in a single cell passing by two planar electrodes that are separated by a nano-gap. The cell experiences an electric field that changes in time, as it goes over the electrodes in the channel. The nano-gap between the electrodes enhances the electric field's strength in the micro-channel, thus enabling the use of low potential difference between the electrodes. By computing the electric field on the surface of the cell we can calculate the pore density, as predicted by the model described by Krassowska and Filev (Biophys. J. 92(2):404-417, 2007). The simulation presented in this article is a useful tool for planning and executing experiments of single-cell electroporation in flow-through devices. We demonstrate how different parameters, such as cell size and the size of the gap between the electrodes, change the pore density and show how electroporation between micro-electrodes on the same plane is different from conventional electroporation between facing electrodes.