Pelagic fishes are among the most ecologically and economically important fish species in European seas. In principle, these pelagic fishes have potential to demonstrate rapid abundance and distribution shifts in response to climatic variability due to their high adult motility, planktonic larval stages, and low dependence on benthic habitat for food or shelter during their life histories. Here, we provide evidence of substantial climate-driven changes to the structure of pelagic fish communities in European shelf seas. We investigated the patterns of species-level change using catch records from 57 870 fisheries-independent survey trawls from across European continental shelf region between 1965 and 2012. We analysed changes in the distribution and rate of occurrence of the six most common species, and observed a strong subtropicalization of the North Sea and Baltic Sea assemblages. These areas have shifted away from cold-water assemblages typically characterized by Atlantic herring and European sprat from the 1960s to 1980s, to warmer-water assemblages including Atlantic mackerel, Atlantic horse mackerel, European pilchard and European anchovy from the 1990s onwards. We next investigated if warming sea temperatures have forced these changes using temporally comprehensive data from the North Sea region. Our models indicated the primary driver of change in these species has been sea surface temperatures in all cases. Together, these analyses highlight how individual species responses have combined to result in a dramatic subtropicalization of the pelagic fish assemblage of the European continental shelf.