In this paper, robust fault diagnosis problem of Proton Exchange Membrane Fuel Cells (PEMFC) is presented based on Takagi-Sugeno (TS) Fuzzy Unknown Input Observer (FUIO). TS FUIO based on Linear Matrix Equalities (LMEs) and the Linear Matrix Inequalities (LMIs) are design. Firstly, the nonlinear PEMFC system with sensor faults and disturbance is represented by TS fuzzy model. Then, a FUIO and sensor fault estimation algorithm is developed and then a model based Fuzzy Fault Tolerant Controller design uses the concept of Parallel Distributed Compensation (PDC). Sufficient stability conditions are studied based on LMIs and LMEs. In order to verify the proposed approach, a PEMFC system with return manifold pressure and hydrogen mass sensors fault and disturbance was tested to illustrate the effectiveness of the proposed strategy. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.