Since the traditional fault diagnosis method of the marine fuel system has a low accuracy of identification, the algorithm solution can easily fall into local optimum, and they are not fit for the research on the fault diagnosis of a marine fuel system. Hence, a fault diagnosis method for a marine fuel system based on the SaDE-ELM algorithm is proposed. First, the parameters of initializing extreme learning machine are adopted by a differential evolution algorithm. Second, the fault diagnosis of the marine fuel system is realized by the fault diagnosis model corresponding to the state training of marine fuel system. Based on the obtained fault data of a marine fuel system, the proposed method is verified. The experimental results show that this method produces higher recognition accuracy and faster recognition speed that are superior to the traditional BP neural network, SVM support vector machine diagnosis algorithm, and the un-optimized extreme learning machine algorithm. The results have important significance relevant to fault diagnosis for a marine fuel system. The algorithm based on SaDE-ELM is an effective and practical method of fault diagnosis for a marine fuel system.