The outrigger structural system is one of the most widely used lateral load-resisting structural systems for high-rise buildings. To increase the energy dissipation capacity of the outrigger system, an outrigger damping system has been proposed as a novel energy dissipation system. In this system, the outrigger and perimeter columns are separate and vertical viscous dampers are equipped between the outrigger and perimeter columns. In this study, the control performance of a semi-active outrigger damping system for the seismic protection of a building structure was investigated. Semi-active damping devices, such as magnetorheological (MR) dampers instead of passive dampers, are installed vertically between the outrigger and perimeter columns to achieve large and adaptable energy dissipation. A fuzzy logic control algorithm was used to generate a command voltage sent to the semi-active MR dampers. A genetic algorithm was used to optimize the fuzzy logic controller. An artificial earthquake load was generated for the numerical simulation and a simplified numerical model of a damped outrigger system was developed. Numerical analyses showed that the semi-active damped outrigger system could effectively reduce both the displacement and acceleration responses of the tall buildings compared to a passive outrigger damper system.