A method of controlling an Automatic Guided Vehicle (AGV) system includes setting moving paths of the AGVs by taking into account task performing costs of cases for orders of all tasks to be performed by the AGVs, and controlling the AGVs according to the set moving paths. The setting of the moving paths includes calculating the cases for the orders of all the tasks to be performed by the AGVs calculating respective costs required for the AGVs to perform the tasks for the calculated cases, calculating the task performing costs using the respective costs, and setting the moving paths of the AGVs according to a case where a minimum one of the calculated task performing costs is incurred.