The paper proposes an intelligent control of DC–DC boost converter in the presence of uncertain dynamics. The converter is desired to operate with an energy harvesting system, where the input conditions are uncertain. An extended state observer (ESO) is designed which estimates and accords with the disturbances caused by load and input uncertainties. The proposed control technique address the issues of uncertainties involved in the energy harvesting system where the system is connected to constant voltage source. The overall stability of the system is proved. The effectiveness of the proposed strategy is verified for a representative example and it assures fast voltage regulation, even in the presence of sudden load and input voltage changes. This proves that the proposed method is capable of compensating the uncertain dynamics in the system. © Springer International Publishing Switzerland 2016.