This paper proposes a new control strategy and a novel modulation technique for a grid-connected photo-voltaic (PV) system using a single-phase five-level flying capacitor (FC) based active-neutral-point-clamped (ANPC) converter. The proposed modulator can control the FC voltage to follow the requested reference value and simultaneously generate the required ac output voltage regardless of the values of the dc capacitor voltages of the converter. By implementing this method, smaller values of dc-link and flying capacitors can be used even in applications that could experience ripple or transient in the capacitors voltage. In the grid-connected single-phase five-level ANPC, where the capacitors can experience pulsation power and dc-link balancing issues, the selection of the reference voltage value for the FC can play an important role to balance the average values of the dc-link capacitors voltage. The proposed new control strategy uses a new reference voltage for the FC to be applied by the new modulator to have an average balanced dc-link voltages as well as an ac output voltage with good power quality. Simulation studies demonstrate the effectiveness of the proposed modulation technique and control strategy even with using relatively small dc capacitors to produce high quality output voltage and current and maintaining an average balanced dc-link voltages.