This paper applies an active period based bottleneck detection method to flow shop manufacturing system with limited buffer size. Manufacturing systems are constrained by one or more bottlenecks which degrades the system throughput. Conventional bottleneck detection methods include the waiting time or queue length of production stations and their utilization. Due to the random events such as production time of items, machine failure and repair times, the systems may change over time, and subsequently bottlenecks shift from one station to another station. Active period of working station may cause other stations to wait for productions. Information when and where active periods occur helps to find bottlenecks in production systems. Based on these informations, we predict bottlenecks in applying AweSim simulation language. We compare the simulation results of conventional methods with those obtained from duration of active period method, and duration ratio method of both sole and shift bottleneck periods. Even though simulation results are from simple flow shop model, they are quite promising for predicting bottlenecks of production stations. We hope this study aids in decision making regarding the improving system production yield and allocation of available resources of system.