A control system for a multilevel converter includes a differential mode current regulator, a neutral point (NP) controller and a PWM controller for generating switching pulses for the multilevel converter. The differential mode current regulator generates reference voltage command signals based on a difference between reference current command signals and actual current command signals, and the NP controller determines a modified neutral point current signal in response to a DC link voltage unbalance. The NP controller utilizes the modified neutral point current signal to generate a common mode reference voltage signal. The switching pulses are generated by the PWM controller based on the reference voltage command signals and the common mode reference voltage signal.