Although a significant amount of simulation research has been carried out for design and analysis of flexible manufacturing systems (FMS), it does not provide optimal solutions. In this research, we employ two optimum-seeking methods to design and optimize a manufacturing system. The first method is a Taguchi approach, which uses robust design concept to reduce the output variation. The second method is the response surface methodology (RSM), which combines mathematical and statistical techniques to study the geography of the response surface. The results show that throughput of a selected FMS system can be maximized when both methods are employed.