Several manufacturing industries try to reduce transportation waste using automated material handling systems, which can enhance the transportation of raw materials from one location to another in the production line of a manufacturing area. The issue with transportation and job flow is a critical factor in a production line because some production stations need to wait for the work-in-progress to be delivered. Automated guided vehicle (AGV) transportation needs a setup of traffic control over a factory’s physical infrastructure and simulation. Doing so can help showcase and evaluate possible deficiencies that can be improved in the real job flow scenario of the production line. The design of experiment plays a huge role in finding and explaining variations of information under conditions that are regularly put as a hypothesis to reflect or describe the variation. A simulation model is implemented by adopting simplified AGV parameters. The model development follows the structure of system specification → machine specification → AGV specification → discrete-event simulation model → experimental design → analysis of performance indicators (PIs). To precisely reflect an alternative for evaluating aforementioned issues, this study proposes the model stated above and an analysis that is based on the PIs. Analysis of variance (ANOVA) results are chosen to analyze different factors affecting the PIs. Using the factorial ANOVA test results, this study uses one-way and two-way interactions to compare the relationship between job flow time, AGVs, AGV utilization, number of AGVs, and average waiting time.