This paper presents two control design strategies for voltage regulation in a single inductor dual-output DC-DC buck converter system. Based on a nominal multiple input multiple output plant model and performance requirements, both a Linear Quadratic Regulator and a Decoupled PI control law are designed to control the power converter system under parametric uncertainties such as voltage source variation, constant power load variation, and load resistance variation. Therefore, the converter can cascade operation, which may cause the undesired effects of voltage oscillation and reduce the system’s stability margin. The control performance was assessed under both the uncertainties of resistive loading and the power variation in a constant power load. A single inductor dual-output DC-DC buck converter board was developed for experimental tests. The experimental results show that the Linear Quadratic Regulator strategy, compared to the PI strategy, presented a robust performance in the presence of parametric uncertainties in the resistive load-bearing; however, it was sensitive to uncertainties due to the presence of constant power loads.