Pelagic fauna is expected to be impacted under climate change according to ecosystem simulations. However, the direction and magnitude of the impact is still uncertain and still not corroborated by observation-based statistical studies. Here we compile a global underwater sonar database and 20 ocean climate projections to predict the future distribution of sound-scattering fauna around the world’s oceans. We show that global pelagic fauna will be seriously compromised by the end of the twenty-first century if we continue under the current greenhouse emission scenario. Low and mid latitudes are expected to lose from 3% to 22% of animal biomass due to the expansion of low-productive systems, while higher latitudes would be populated by present-day temperate fauna, supporting results from ecosystem simulations. We further show that strong mitigation measures to contain global warming below 2 °C would reduce these impacts to less than half.