The success of military operations mainly relies on the proper flow of the logistical supplies such as water, food, ammunition, etc. from source to the operation theater on time. There are special types of transportation vessels regarding the feature of supply. However, when transporting special material like ammunition, most navies usually prefer utilizing their own transportation capabilities since they require special treatment. For this reason, such material is carried in special boxes, called containers. To minimize the transportation cost and time, an efficient container stowage plan is necessary in terms of loading and unloading these containers. This chapter aims to develop a solution methodology to the problem with the focus on military logistics planning. For this purpose, the author develops a mathematical model that attempts to minimize the transportation time by creating proper loading and unloading sequence of containers to military cargo ships.