Fuel cell (PC) is an efficient energy conversion technology that is growing rapidly and will have a significant role to play in a number of energy end-use sectors, from small-scale applications to large-scale power plants. In this paper, two new methods for voltage harmonic compensation of a stand-alone single phase inverted-based PC are presented and evaluated. The stand-alone power system under study consists of: 1) Proton-Exchange-Membrane (PEM) PC with unidirectional DC/DC converter, which converts the DC voltage delivered by the FC to the DC bus voltage; 2) single-phase pulse width modulated (PWM) inverter; 3) transformer; 4) passive filter; and 5) linear and non-linear loads. The dynamic model of this system and the non-sinusoidal output-based controls applied to the PWM inverter for voltage regulation and harmonic compensation are detailed in this paper, and evaluated by simulation under different linear and non-linear loads. Simulation results show the effectiveness of the two purposed methods for voltage harmonic compensation to acceptable levels defined in grid codes. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.