This study presents synchrophasor assisted protection scheme for the protection of long transmission line compensated with shunt flexible AC transmission system (FACTS) device. With the advancement in synchrophasor technology, data communication medium, and wide area measurement system for transmission line protection, the differential protection scheme is a most suited scheme over the over-current, distance and directional protection schemes. The proposed scheme discriminate between internal and external fault using the time synchronised voltages and currents of both the terminal of the transmission line. The performance of proposed scheme has been evaluated on IEEE 12 bus FACTS benchmark power system model implemented in PSCAD/EMTDC. The measured voltage & current signals are pre-processed and phasors are estimated through DFT algorithm in MATLAB. The performance remains unaffected during wide variation in fault and system parameters including different line length and static var compensator rating. The test results confirm the selective, simplicity, high speed, sensitivity, and robustness of the proposed protection scheme. This scheme is also able to distinguish the faulty phase(s) from healthy phases, which enables the single-pole tripping option. Finally, comparative evaluation of the proposed technique with the existing protection schemes clearly shows its superiority.