In this paper, a high efficiency satellite electrical power supply system is proposed. The increased efficiency of the power supply system allows for downscaling of the solar array and battery weight, which are among the most important satellite design considerations. The satellite power supply system comprises two units, namely a generation unit and a storage unit. To increase the efficiency of the solar array, a maximum power point tracker (MPPT) is used in the power generation unit. In order to improve the MPPT performance, a novel algorithm is proposed on the basis of the hill climbing method. This method can track the main peak of the array power curve in satellites with long duration missions under unpredicted circumstances such as a part of the array being damaged or the presence of a shadow. A lithium-ion battery is utilized in the storage unit. An algorithm for calculating the optimal rate of battery charging is proposed where the battery is charged with the maximum possible efficiency considering the situation of the satellite. The proposed system is designed and manufactured. In addition, it is compared to the conventional power supply systems in similar satellites. Results show a 12% increase in the overall efficiency of the power supply system when compared to the conventional method.