In the previous paper, the authors introduced a concept of 'mission-effectiveness' for evaluating the effect of seakeeping performance on ship system capability. They also showed that the short-term mission-effectiveness could be estimated easily by applying a simple method proposed. In the present paper, they show the importance of long-term mission-effectiveness and propose two methods for estimating long-term mission-effectiveness. One is the statistical prediction method which estimates long-term availability of the ship system for a single mission, and the other the simulation method which gives the overall mission-effectiveness for a combined mission as well as a single mission. They discuss the long-term mission-effectiveness of patrol boats which are assumed to be operated for the mission “Salvage”.