Electroporation is one of the most popular nonviral gene transfer methods for embryonic stem cell transfection. Bulk electroporation techniques, however, require a high electrical field and provide a nonuniform electrical field distribution among randomly distributed cells, leading to limited transfection efficiency and cell viability, especially for a low number of cells. We present here a membrane sandwich electroporation system using a well-defined micronozzle array. This device is capable of transfecting hundred to millions of cells with good performance. The ability to treat a small number of cells (i.e., a hundred) offers great potential to work with hard-to-harvest patient cells for pharmaceutical kinetic studies. Numerical simulation of the initial transmembrane potential distribution and propidium iodide (PI) dye diffusion experiments demonstrated the advantage of highly focused and localized electric field strength provided by the micronozzle array over conventional bulk electroporation.