Traditional sliding mode controller applied to a DC/DC boost converter for the improvement and optimization of the proton exchange membrane fuel cell (PEMFC) system efficiency, has the drawback of chattering phenomenon. Thus, based on the analysis of the mathematical model of PEMFC, this paper addresses the second order super twisting algorithm (STA) as a solution of chattering reduction, Stability of the closed loop system is analytically proved using Lyapunov approach for the proposed controller. The model and the controllers are implemented in the MATLAB and SIMULINK environment. A comparison of results indicates that the suggested approach has considerable advantages compared to the classical sliding mode control. (C) 2016 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.