In order to increase the power transfer and providing the optimum utilisation of the power system capability, application of flexible alternating current transmission system (FACTS) devices technology, such as static synchronous compensator (STATCOM), has been attracted, in recent years. However, the STATCOM changes the voltage and current of the power system that disturb the operation of the impedance-based synchronous generator loss of excitation (LOE) protection. Then, this study proposes a new flux-based LOE protection method, in the presence of STATCOM, that is based on the local variation of the flux linkage of the generator available at the location of relay. The mentioned relay is independent of other generator protection relays without any coordination. In order to show the satisfying operation of the proposed method, some simulations have been carried out in the Matlab/Simulink software. A single-machine infinite bus and a three-machine infinite bus systems have been used in simulations. The results show that the presence of STATCOM has no important effect on the performance of proposed relay opposite to a negative offset relay with two protective zones (the widely used impedance method) which is affected by STATCOM operation.