This paper presents an extension of the Selective Harmonic Elimination Model Predictive Control (SHE-MPC) to a Flying Capacitor (FC) converter with FC-type capacitor balancing. The SHE-MPC strategy ensures fast closed-loop dynamics by slightly modifying the optimal SHE-PWM pattern during transients while effectively canceling low-order harmonics in a steady state. Simulation results comparing SHE-MPC with standard Finite Control Set Model Predictive Control (FCS-MPC) demonstrate superior steady-state tracking and harmonic elimination capabilities of SHE-MPC over FCS-MPC. Additionally, transient state behavior analysis reveals similar dynamic response times between the two strategies. Future work will explore the optimization of internal switching states and efficiency improvements.