Climate change is a pressing threat to marine life, global fisheries, and the communities that depend on them. Effective resource management under increasing climate impacts requires robust assessments of species and ecosystem risk. For a highly migratory pelagic species of high commercial value, such as Pacific bluefin tuna (Thunnus orientalis), intense fishing pressure compounded by climate change poses a significant threat to long-term population and fishery sustainability. Here, we applied a novel climate risk index for marine biodiversity that integrates (1) species distribution, (2) sensitivity to climate stressors, and (3) adaptive capacity to assess species vulnerability and absolute risk under contrasting low (SSP1-2.6) and high (SSP5-8.5) emission scenarios. We leveraged publicly available occurrence records from 2000–2024 to model habitat preferences of bluefin tuna across the North Pacific Ocean using a generalized linear mixed model framework with spatial random effects. We incorporated feeding ecology and environmental predictors accounting for the vertical structure of the water column to predict suitable habitat in productive surface waters (≤100 m) and deeper habitats (>100 m). For each depth layer across the predicted distribution, we used future climate projections to estimate climate vulnerability and risk to local population persistence. Overall, Pacific bluefin tuna was designated as facing high climate risk under both emission scenarios, with 16.1% of predicted habitat classified as critical risk under the high-emissions scenario (12.5% under low emissions), indicating substantial future climate impacts across the species’ range. By mapping critical vulnerability areas, we identified regions likely to require enhanced conservation measures, including Kuroshio-influenced waters of southern Japan, the East China Sea, and other low-latitude regions of the North Pacific. Our analysis contributes to growing evidence of climate-driven risks to key fisheries species and emphasizes the need for adaptive management, targeted conservation, and long-term monitoring to track shifts in climate risk in the North Pacific Ocean and beyond.