This paper focuses on observer based fault reconstruction for a class of nonlinear uncertain systems with Lipschitz nonlinearities. An adaptive-gain Super-Twisting (STW) observer is developed for observing the system states, where the adaptive law compensates the uncertainty in parameters. The inherent equivalent output error injection feature of STW algorithm is then used to reconstruct the fault signal. The performance of the proposed observer is validated through a Hardware-In-Loop (HIL) simulator which consists of a commercial twin screw compressor and a real time Polymer Electrolyte Membrane fuel cell emulation system. The simulation results illustrate the feasibility and effectiveness of the proposed approach for application to fuel cell systems.