Summary Unified power flow controller (UPFC) flexible alternating current transmission system devices affect voltage and current signals at beginning of the feeder when a fault occurs. This indicates importance of fault location in compensated transmission lines. In the proposed method, only voltage signal of one terminal is employed. When a fault occurs, three‐fourth cycle of the voltage signal is received at one side and then the signal is divided into four separate partitions. Then, fast discrete orthonormal stockwell transform is applied to each partition to extract a feature vector. Using 10 first principle component analysis values of the feature vectors and Gaussian process regression, fault location is estimated. The proposed method is evaluated on a 500 kV transmission line of 300 km length with UPFC at different positions of the transmission line. Different conditions including fault inception angle, numerical references of UPFC and its operating modes, load existence, sampling frequency, and presence of noise are investigated. Numerical results under different conditions indicate high accuracy and efficiency of the proposed method.