PurposeIn the real world many companies combine the operations of manufacturing, assembly and disassembly. Thus, the integration of just‐in‐time FMS, FAS, and flexible disassembly system (DAS) models poses an interesting problem. The purpose of this paper is to provide major emphasis on a new simulation model for design and performance evaluation of a flexible assembly and disassembly system with dual Kanban under a stochastic system. This paper also primarily investigates the effect of varying the number of kanban cards, mean inter‐arrival time of demand and locations of the bottlenecks on the performance integration of JIT flexible manufacturing, assembly and disassembly systems.Design/methodology/approachSimulation is carried out in ARENA and data is analyzed using multivariate analysis of variance (MANOVA). This paper investigates the effect of varying number of kanban cards, mean inter‐arrival time of demand, and locations of the bottlenecks on the performance integration of JIT flexible manufacturing, assembly and disassembly systems. The performance measures that are simultaneously considered are the fill rate, work in process, and mean cycle time. This paper emphasizes that understanding the interactions between the variables and their effects on system performance is of utmost importance for managers in improving performance processes.FindingsIn manufacturing practice, there are many industrial units that represent the mixture of the referred three models. This paper presents a new simulation model for design and performance evaluation of a flexible assembly and disassembly system with dual kanban. The simulation results are statistically compared with MANOVA. MANOVA is used to perform the test with multiple objective functions, e.g. with the average production cycle time, percentage average fill rate, and work‐in‐process. The conclusion to be drawn is that minimized WIP can be obtained by higher percentage average fill rate, lower WIP, small average part cycles times, and increasing in kanban cards while simultaneously retaining full customer satisfaction.Originality/valueThe researcher presents the newly developed kanban system into the production system of JIT flexible manufacturing, assembly and disassembly system with simulation technique. Furthermore, by assigning time factors to the models, several performance measures can be easily computed. Then, the researcher tests the effect of the number of kanban card on integration of JIT flexible manufacturing, assembly and disassembly systems using a simulation approach, the simulation model is developed using the ARENA simulation package. The results are applied to a small case study. For a single product under the integration of JIT flexible manufacturing, assembly and disassembly systems, as the number of kanban cards increase, the fill rate along with work in process and the mean cycle time increases as well.