This simulation-based experimental study focuses on the performance of stochastic flexible manufacturing system with Automated Guided Vehicles AGVs. Four levels of AGV fleet size (i.e. 1 AGV, 2 AGVs, 3 AGVs and 4 AGVs) at four different AGV velocities (i.e. 2 m/s, 4 m/s, 6 m/s and 8 m/s) with four sequencing rules are used to perform the experiments. The performance of the system is measured by two performance measures like make-span time and resource utilization. It is observed that the performance improves as the numbers of AGVs increases in all combinations and this increase is more visible when the system runs with 2 AGVs instead of 1 AGV. The impact of AGV velocity is found to be more visible with the use of more number of AGVs. There was effect of sequencing rules for different combinations of number of AGVs and velocities.