Discrete-event simulation has been recognized as an invaluable tool in analyzing and designing FMSs. In this dissertation, a computer-aided simulation tool based on Petri nets is presented to facilitate simulation projects in the manufacturing area. For modeling and simulation of FMSs, Conserved nets which are a subclass of Petri nets are proposed and implemented. The structural characteristics and liveness conditions of Conserved nets are investigated. While hardware components are modeled by hierarchically-classified Petri net objects, high-level, real-time control systems in FMSs are separately modeled and integrated with a Petri net model to resolve conflicts occurring in Petri net execution. The structure of the Petri net-based simulation tool is presented. Also, the use of the simulation tool is illustrated with several case studies including performance comparison of push- and pull-based AGV dispatching rules in an FMS. Finally, strengths and weaknesses of the developed simulation tool are discussed including areas for future study.