We studied the molecular transfer to the nucleus in an on-chip cell electroporation using focused electric field. The microdevice consisted of a cell culturing well and eight microchannels that had micro-orifices for electric field focusing and cell trapping. The micro-orifice was integrated in a vertical wall of the microchannel to visualize the process of molecular transfer with the confocal fluorescence microscopy. HeLa cells suspended in a phosphate buffered saline including ethidium homodimer and Qdot 525 was introduced into the cell culturing well and cells were trapped at the micro-orifices. Then, pulsed voltage in the range of 1-10 V was applied for 500 ms between Ag/AgCl electrodes that were inserted in the cell culturing well and the outlet of a microchannel. We visualized pore formation and nucleus membrane using the red fluorescence from ethidium homodimer. We observed the increase in the fraction of Qdot 525 translocated into the nucleus as the distance between the orifice and the nucleus membrane decreased. This finding indicated that the molecular permeability of nucleus membrane was increased by the focused electric field in the vicinity of the micro-orifice.