The nonlinear operation of metal oxide varistor (MOV)-protected series compensator in transmission lines introduces complications into fault detection approaches. The accuracy of a conventional fault detection schemes is adversely affected by continuous change of the system impedance and load current at the point of a series compensation unit. Thus, this study suggests a method for detecting the faulted phase in MOV-protected series-compensated transmission lines. Primarily, the fault feature is identified using the covariance coefficients of the current samples during the fault period and the current samples during the pre-fault period. Furthermore, a convenience fault detection index is established by applying the cumulative sum technique. Extensive validation through different fault circumstances is accomplished, including different fault positions, resistances, and inception times. The experimental results show that the proposed method performs well with high resistance or impedance faults, faults in noisy conditions, and close-in and far-end faults. The proposed method is simple and efficient for faulty phase detection in MOV-protected series-compensated transmission lines.