A kind of fault diagnosis system of molten carbonate fuel cell (MCFC) stack is proposed in this paper. It is composed of a fuzzy neural network (FNN) and a fault diagnosis element. FNN is able to deal with the information of the expert knowledge and the experiment data efficiently. It also has the ability to approximate any smooth system. FNN is used to identify the fault diagnosis model of MCFC stack. The fuzzy fault decision element can diagnose the state of the MCFC generating system, normal or fault, and can decide the type of the fault based on the outputs of FNN model and the MCFC system. Some simulation experiment results are demonstrated in this paper.