Seabird bycatch by the longline fisheries of the Pacific Ocean is a major conservation concern. However, relatively few studies have examined the impacts of distant water longline fishing on the high seas due to the difficulty associated with deploying observers. Our study addresses this data gap by analyzing data from 2666 Taiwanese scientific observation data sets from 2002 to 2007 to calculate the seabird bycatch rate and to estimate the mortality of seabirds as a result of fishing activities by the entire fleet. A total of 379 seabirds were caught and 88% were albatross. A negative binomial distribution was used to represent the observed data based on spatial and temporal stratification, which yielded bycatch rates that ranged from 0.0003 to 0.2213 birds per 1000 hooks. The bycatch rates were highest in the areas between 25–45°N and 165°E–160°W between October and March and the areas between 25–35°S and 170°E–165°W between April and September. Using the observed data for bycatch rates and total fishing effort, the estimated number of seabird deaths caused by the Taiwanese fleet ranged from 1120 to 4290 birds annually. Increasing the observer coverage of specific fleets and areas, prioritizing observer programs and combined with international cooperation in research, would improve bycatch calculations. Seabird conservation efforts can be improved by monitoring fishing effort and the mandatory implementation of multiple mitigation measures.