Robust output tracking control of a linear DC brushless motor for transportation within a manufacturing system is presented. System identification for a linear motor with a driver is performed by a dynamic signal analyser, thus providing a linearised model for the motor. According to the selected nominal parameters, an optimal solution with a prescribed degree of stability is obtained. Due to identification procedures and possible payload variations, parameter uncertainties exist. Thus, an auxiliary input, connected to the nominal optimal control, is introduced to guarantee robustness for the output tracking control problem. A computer simulation and experimental implementation are completed and compared. These results demonstrate the effectiveness of the proposed scheme for output tracking control of the linear DC brushless motor, and also confirm the feasibility of its implementation in industrial applications.