Ancient hyperthermal events in Earth’s history can be used to isolate the evolutionary consequences of climate change and other environmental factors from background geologic intervals. A key biological trait hypothesized to be sensitive to climate change and straightforward to quantify in fossil data is body size, as ectotherms modulate their physiological response to temperature and oxygen change in part through their body size. Here, we measure genus-level extinction and origination selectivity with respect to body size for six extant and ectothermic Linnean classes with robust fossil records (Rhynchonellata, Cephalopoda, Echinoidea, “bony fish”, Bivalvia, and Gastropoda) using occurrence data from the Paleobiology Database. We compare selectivity during background intervals with those during hyperthermal events and their associated recovery intervals spanning the Early Permian to the Recent using capture-mark-recapture models. Using the best-fitting model for each class, we find that background extinction preferentially affects genera with smaller body sizes, whereas hyperthermal events do not show a consistent association between extinction probability and body size. Conversely, genera originating during background intervals are typically larger than average, whereas genera originating during hyperthermal recovery intervals are typically smaller than survivors, except for bony fish, which exhibit preferential origination of larger genera.