This paper first presents hierarchical scheduling and control architecture for a flexible manufacturing cell (FMC) that is currently set up at the Mechanical Industrial Research Laboratories of the Industrial Technology Research Institute at Hsinchu, Taiwan. With this architecture, we focus on the scheduling problem of the FMC and present a scheduling mechanism based on a colored timed Petri net (CTPN) model. The CTPN model has three functions in the proposed mechanism: the first one is to formally describe pallet flows and resource constraints in the FMC by the event‐condition relation; the second one is to analyze conflict points among the pallet flows; the third one is to evaluate the used dispatching rules concerned with the selection of machine routings, the selection of work‐in‐process pallets in inter‐medium buffers and the assignment of the commonly used material‐handling device. Using the CTPN‐based scheduler, anappropriatecombination of dispatching rules for each given batch can be selected to fit given criteria, e.g. minimum batch completion time, maximum resource utilization or minimum tardiness, etc. Moreover, real‐time status of the FMC can be represented in the mechanism for obtaining the on‐line scheduling effect.