A fast heating-up rate generally conflicts with the temperature homogeneity of solid oxide cell (SOC) stacks. This study designs an adaptive model predictive controller (MPC) to regulate the heating-up process of SOC stacks. The controller solves an optimization problem in real time to obtain optimal control that shortens the heating-up time by fully using the safety limit. The controller is verified with a three-dimensional (3D) hotbox–stack model calibrated with experiments. 3D model-in-the-loop (MiL) simulations show that the controller is effective under two heating modes despite of model deviations. Under the electrical heating mode, the controller achieves a 33% acceleration compared with a reference control strategy. Comparisons of electrical and gas heating reveal that the former is 63% faster but the latter consumes 41.6% less energy if the waste heat is fully recovered. The hotbox heat capacity is a major limiting factor for the heating-up process, particularly under the gas heating mode. An 80% reduction in the hotbox heat capacity, which can be achieved by reducing the thickness of the insulation layer, improves the heating-up time and the net energy consumption by 69% and 65% under the gas heating mode, respectively.