Multilevel converters are an attractive alternative for medium voltage applications. The Stacked Multicell Converter (SMC), in particular, is a multilevel converter that allows to increase the output voltage level compared with the classical Flying Capacitor Converter, while decreasing the stored energy in the converter. This paper presents the application of Finite Control Set Model Predictive Control (FCS-MPC) in a three phase SMC with two cells and two stacks. The strategy controls simultaneously the load currents and capacitor voltages. simulation results show that the FCS-MPC strategy produces an effective control of the load current, while keeping balanced capacitor voltages. In addition, it is demonstrated that FCS-MPC outperforms Phase Shifted Pulse Width Modulation with linear controllers in transient and steady state operation.