For high-voltage applications, neutral point clamped-based dual active bridge (NPC-DAB) converters are commonly used. In literature, different fixed phase shift control methods like double phase shift control (DPS), triple phase shift control (TPS), etc., are used to reduce losses in NPC-DAB converter. In this paper, a variable phase shift method is proposed to reduce the losses in the converter. This variable phase shift angle is obtained by utilizing a power loss minimization function in a model predictive controller (MPC). The simulation result shows that MPC based variable phase shift control reduces power loss and improves transient performance in the NPC-DAB system in comparison to PI control based fixed phase shift control.