The fishery compensation by marine spatial planning such as routeing of ships and offshore wind farms is required objective data on whether fishing vessels are engaged in a target area. There has still been no research that calculated the number of fishing operation days scientifically. This study proposes a novel method for calculating the number of fishing operation days using the fishing trajectory data when investigating fishery compensation in marine spatial planning areas. It was calculated by multiplying the average reporting interval of trajectory data, the number of collected data, the status weighting factor, and the weighting factor for fishery compensation according to the location of each fishing vessel. In particular, the number of fishing operation days for the compensation of driftnet fishery was considered the daily average number of large vessels from the port and the fishery loss hours for avoiding collisions with them. The target area for applying the proposed method is the routeing area of ships of Jeju outer port. The yearly average fishing operation days were calculated from three years of data from 2017 to 2019. As a result of the study, the yearly average fishing operation days for the compensation of each fishing village fraternity varied from 0.0 to 39.0 days. The proposed method can be used for fishery compensation as an objective indicator in various marine spatial planning areas.