A low-energy single ion irradiation system is developed in its initiation in Thailand to follow one of the trends in novel ion beam technology exploitation. Single ion irradiation of materials is a highly technological development of ion beam technology. The developed single ion irradiation systems worldwide are primarily in the MeV-energy range and for single cell studies, and recently the trend has been extended to the low-energy range (< 100 keV) but focused on microelectronic applications. Based on our previous research on low-energy ion beam irradiation of biological cells and DNA, we design and simulate a low-energy single ion implantation system, aiming at eventual construction of such a novel ion beam apparatus for applications to the biological studies. In the system, the ion energy is decreased to orders < 1 keV by the existing deceleration lens, then the low-energy ion beam passes through µm slits, and finally, low-energy single ions are obtained by beam scanning with appropriate frequencies from scanner plates and detected by a single ion detection device. Conceptual design, calculation and simulation of this single ion system are presented.