In the previous papers, the authors presented a method for evaluating the seakeeping performance of ships at sea in the initial ship design stage. They introduced 'mission effectiveness' concept as a measure which gave the effect of seakeeping performance on ship system and her missions, and showed it was effective for evaluating the seakeeping performance of ships. They showed too that the short-term mission effectiveness gave the ship's inherent seakeeping performance, and that the long-term mission effectiveness was important to obtain informations for cost/performance trade-off which ship designers as well as ship owners must evaluate in the initial ship planning and design. In the present paper, the authors present a method for estimating the long-term mission effectiveness of ship system, which is to be operated under a mission composed of several different duties, as a function of long-term conditional probability. The long-term mission effectiveness obtained by the present method is compared with that estimated by the simulation method previously. A method for cost/performance evaluation is presented, which gives the mission effectiveness in a broad sense. The present method is applied for the same patrol boats which were used for the numerical examples in the previous papers.