PurposeA major factor to the success of flexible manufacturing systems (FMSs) is their ability to transport work pieces between different workstations. FMS have now become more advanced and material‐handling systems have become progressively more sophisticated, it is not exceptional to have automated steering of tools to workstations as well. Such system design will improve the tool‐handling capability and the system productivity while holding tool cost to a minimum. Tool cost could represent as much as 25 percent of the operating cost. The purpose of this paper is to propose a new colored Petri net (CPN)‐based approach to the design and development of a tool sharing control system that is intended to help use of the proper and minimal number of tools for a manufacturing system.Design/methodology/approachA new black token timed PN model is first developed, to reduce the complexity of the graphical representation a new CPN model is developed. The new CPN model also allows to find the optimal sequence. The optimal sequence has no effect on the work in process (WIP) but it influences the number of tools used in the system. The main input to the PN model for a manufacturing system is the process plan. Next, all the invariants and total number of possible elementary circuits are determined using the Integrated Net Analyzer (INA) software. Output from the INA software is exported to the Excel spreadsheet. The Excel spreadsheet can be designed to calculate the total number of tokens, processing time, cycle time, etc. of each elementary circuit. Subsequently, the constraints used in Lingo will be created according to critical circuit rules. Finally, linear programming (LP) technique is used to optimize the WIP and tool inventory. Lingo software is used for the LP, the constraints from the Excel sheet will be the input data to the Lingo program, and based on those constraints the Lingo will provide the optimal values for the desired parameters. The output from Lingo will be used to recalculate the cycle time of each elementary circuit in the Excel sheet. The system is then analyzed before and after the implementation of the CPN model.FindingsA new CPN model based on tool‐sharing philosophy for an FMS with N part types and M stations is proposed.Originality/valueThe paper presents a new CPN‐based approach to the design and development of a tool sharing control system, that is, intended to help use of the proper and minimal number of tools for a manufacturing system. The new CPN model also allows to find the optimal sequence. The idea is new and pure and has not been presented before using the methodology adopted in this paper.