It is important to maintain high efficiency when charging electrical energy storage elements so as to achieve holistic optimization from an energy generation source (e.g., a solar cell array) to an energy storage element (e.g., a supercapacitor bank). Previous maximum power point tracking (MPPT) methods do not consider the fact that efficiency of the charger varies depending on the power output level of the energy generation source and the state of charge of the storage element. This paper is the first paper to optimize the efficiency of a supercapacitor charging process by utilizing the MPPT technique and simultaneously considering the variable charger efficiency. More precisely, previous MPPT methods only maximize the power output of the energy generation source, but they do not guarantee the maximum energy is stored in the energy storage element. Note that the load device takes its energy from the storage element so it is important to maximize energy transfer from the source into the storage element. We present a rigorous framework to determine the optimal capacitance of a supercapacitor and optimal configuration of a solar cell array so as to maximize the efficiency of energy transfer from the solar cells into a bank of supercapacitors. Experimental results show the efficacy of the proposed technique and design optimization framework.