This paper proposes a hierarchical active power differential signal-based generalized backup protection algorithm using Wide Area Measurement System (WAMS) data for Flexible AC Transmission System (FACTS)-compensated transmission networks. The proposed algorithm can be used for backup protection of transmission systems with any shunt and series-type FACTS devices. The increased number of FACT compensators affects the reliable operation of primary and backup protection of the transmission lines. Both shunt and series compensated lines cause malfunctioning of existing backup protection schemes. The proposed algorithm utilizes the sequence components of bus voltages and active power differential signals of lines to identify the faulty line. The algorithm is validated on a modified 9-bus system under MATLAB/SIMULINK platform. It is observed that the algorithm is suitable for identifying a faulty line in transmission systems containing both uncompensated and compensated lines with series or shunt-type FACTS controllers. This algorithm has the advantage that it uses a generalized backup protection logic and can be used for the accurate identification of a faulty line irrespective of the type of compensation devices.