This work presents an active voltage balancing controller for flying capacitor multilevel (FCML) converters intended for parallel operation with high-bandwidth current controllers. The parallel control architecture is derived from a state-space averaged plant model of the converter and is designed to decouple the dynamics of the inductor current and flying capacitor voltages. A design methodology is presented for the flying capacitor voltage and inductor current controllers accounting for their mutual interaction. Experimental results demonstrating closed-loop control responding to line and load transients are presented.