This paper deals with Five-Level Flying Capacitor Multilevel Inverter (FCMLI) based Static Synchronous Series Compensator (SSSC) as used for the series compensation of transmission line. Here, voltage is injected in series with the transmission line. It is preferred to other compensating devices because apart from controlling the active and reactive power flow, it helps to damp out unwanted oscillations, such as reducing the Sub-Synchronous Resonance (SSR), Ferro-resonance and thus helps in improving the Power Quality (PQ). Hence, FCMLI is used which helps to ameliorate the output waveform and reduces the auxiliary filtering requirements. Moreover, the control logic for the inverter that has been shown in such a way that voltage stress across each capacitor connected to DC-link voltage is equal. The control logic has been implemented in MATLAB/Simulink environment and the result is shown as there are no SSR phenomena and considerable less line loss.