A bonded warehouse is the warehouse located in bonded area. It functions not only as a general warehouse but also as a place for managing the work related to import and export bonded goods. As a general warehouse, it uses the rack system to store the goods and the folk lift truck to move the unitized goods. The operation of the storing system closely related to the efficiency of space uses in a warehouse and vehicle working. Thus, vehicle performance measured in distance units in the ware-house could be used as one of the key performance measure in warehouse system. This paper focuses on the operation efficiency of the bonded warehouse which uses rack system for the storing and the folk lift truck for moving goods. The method of load allocation for balancing the rack uses and vehicle operation for maximizing efficiency are the specific concerns in this paper. The simulation study is conducted to find a policy for efficient vehicle operation based on balanced rack utilization, and the favorable result for the system operation would lead the usable proposal in vehicle operation.