There are a large number of photovoltaic (PV) arrays in large-scale PV power plants or regional distributed PV power plants, and the output of different arrays fluctuates with the external conditions. The deviation and evolution information of the array output are easily covered by the random fluctuations of the PV output, which makes the fault diagnosis of PV arrays difficult. In this paper, a fault diagnosis method based on the deviation characteristics of the PV array output is proposed. Based on the current of the PV array on the DC (direct current) side, the deviation characteristics of the PV array output under different arrays and time series are analyzed. Then, the deviation function is constructed to evaluate the output deviation of the PV array. Finally, the fault diagnosis of a PV array is realized by using the probabilistic neural network (PNN), and the effectiveness of the proposed method is verified. The main contributions of this paper are to propose the deviation function that can extract the fault characteristics of PV array and the fault diagnosis method just using the array current which can be easily applied in the PV plant.