To improve the accuracy and portability of fault location in secondary circuits of smart substations, a fault location method for secondary circuits based on graph neural networks is proposed. First, a fault analysis of the secondary circuits in smart substations is conducted, and a graph database model of the secondary circuits is constructed, revealing the connection relationships between the secondary devices. Then, the fault location problem in secondary circuits is defined as a graph classification problem, and a fault graph generation model is proposed based on a representation method for fault information in secondary circuits. Finally, a fault location model for secondary circuits based on graph neural networks is constructed, and a performance optimization method based on binary cross-entropy is proposed to achieve accurate fault location in substation secondary circuits. Using the secondary circuits of a 220 kV smart substation as a reference, different case studies of secondary circuit faults are generated by altering the network topology, connection relationships, and network configurations through the fault graph generation model. Experiments comparing the proposed location method with other models show that this method has higher location accuracy and robustness.