Navy surface vessels require pier services such as emergency repair, oil supply, arm loading/unloading, craning, standby readiness, normal repair, gun arrangement, ammunition loading, and food loading during the period in port. The purpose of this study is to establish efficient berth allocation plan for navy surface vessels in home port under the limited resources of piers and equipments. This study suggests Mixed Integer Programming model for berth allocation problem, considering precedence relationships among services and the uncertainty of the arrival and departure for each vessel. For an effective analysis, the model is implemented by ILOG OPL(Optimization Programming Language) Studio 6.0 and ILOG CPLEX 11.1., which shows a reasonable result.