CubeSat is a nanosatellite platform that provides access to space for small payloads. It is an attractive solution for space exploration missions as it reduces cost and development time. However, size constraints restrict the surface area for solar panels and thus the generated power. The efficiency of the power condition modules of the electrical power system (EPS) is a relevant feature in the design of a CubeSat. One of the parameters that defines the efficiency of the power converters is their operating input and output voltages; these voltages are given by the array configurations of solar cells and battery cells according to the number of series or parallel connected cells. Therefore, we selected four solar array and battery package combinations for a 3U CubeSat with body mounted solar cells and compared losses and efficiency of the converter by calculation and experimentation. The results reveal that the highest efficiency values for load power values between 0.7W and 7W are about 98% for input voltage of 7.5V and output voltage of 6.6V. The best array configuration is derived due to these results: two string of three serial connected solar cells and a stack of two batteries in serial connection. These results allow us to design an efficient electrical power system for a 3U CubeSat; thus, the loads and the batteries received most of the provided energy by the solar array.