This study aims to model, analyze, and evaluate performance of a flexible manufacturing system, constituting a carousel-based manufacturing and assembly cells layout, configured to produce mixed-model multiple products employing inter-/intra-cellular routing flexibility in which manufacturing and assembly resources are subject to working and failure modes. A hierarchical colored Petri net model is developed to analyze performance of the flexible manufacturing system. Colored Petri net modeling experiments have been conducted to evaluate the system performance for throughput, cycle time, and work-in-process. The system performance has been investigated in relation to material supply and handling system, process execution, and production resources reliability variables. Different input factors are considered for simulation modeling such as mean machining time, mean loading/unloading time, mean assembly time, buffer capacity, material supply inter-arrival time, number of operations between failures, and mean time to repair for production resources; a variation in input factors has shown a significant impact on system performance measures. The colored Petri net–based modeling, simulation, and analysis approach has been demonstrated as an efficient method for carousel-based mixed-model configured flexible manufacturing system.