This paper presents a System-on-Chip approach (SoC), exploiting the availability and capacity of SRAM-based FPGA technology to design and implement an on-board computer system (OBC) for use in low earth orbit (LEO) nano-satellite. This work is part of a University project that aims to develop the first Moroccan university nano-satellite based on the “CubeSat” standard. As such, the proposed OBC is designed to provide a payload and a testbed for space-based reconfigurable platform. The hardware and software reconfigurable architecture of the system is based on Xilinx's Spartan-6 FPGA. The proposed design of the OBC takes into account the constraints inherent to space environment (sensitivity to ionizing radiation), and uses mitigation techniques that combine hardware and software redundancy to improve system availability and reliability. The paper also presents the guidelines for possible implementation.