Allocating buffers in manufacturing systems is one of easiest ways to improve the throughput of the system, as changes can be implemented quickly and the initial cost of the change is low. Yet, while an increase in the buffer size usually increases the throughput, it often also increases the work in progress and the makespan, therefore increasing the inventory and the time to the customer. Subsequently, the trade off between the throughput, the work in progress, and the makespan are of significant research interest. This paper describes a general prediction model of these performance measures for different buffer size increases based on only a single simulation. A fully automated implementation of the simulation analysis and prediction model for manufacturing systems of any size and complexity is available. The method can be used for flow shops, job shops, and serial or parallel systems.