This paper presents two control design strategies for voltage regulation in a single inductor dual output (SIDO) DC-DC Buck converter system. Based on a nominal multiple input multiple output (MIMO) plant model and performance requirements, both an LQR and a decoupled PI control laws are designed to control the power converter system, under parametric uncertainties such as voltage source variation, CPL power variation, and load resistance variation. Therefore, the SIDO converter can cascade operating, which may cause the undesired effects of voltage oscillation and reduce the system's stability margin. The control performance was assessed under both uncertainties resistive loading and power variation of a constant power load (CPL). A SIDO DC-DC Buck converter board has been developed for experimental tests. The experimental results show that the LQR strategy, compared to the PI strategy, presented a robust performance in the presence of parametric uncertainties in the resistive loads being, however, sensitive to uncertainties due to the presence of CPL loads.