A new and advanced control system for three-dimensional (3D) overhead cranes is proposed in this study using state feedback control in discrete time to deliver high performance trajectory tracking with minimum load swings in high-speed motions. By adopting the independent joint control strategy, a new and simplified model is developed where the overhead crane actuators are used to design the controller, with all the nonlinear equations of motions being viewed as disturbances affecting each actuator. A feedforward control is then designed to tackle these disturbances via computed torque control technique. A new load swing control is designed along with a new motion planning scheme to robustly minimize load swings as well as allowing fast load transportation without violating system’s constraints through updating reference trolley accelerations. The stability and performance analysis of the proposed discrete-time control system are demonstrated and validated analytically and practically.