Climate change in mountain regions has exposed high-elevation species to rapidly changing temperatures. Although climate exposure can be reduced in certain microclimates, the quality of microclimatic refugia might also degrade with climate change. The American pika (
Ochotona princeps) often inhabits high elevations, and is considered climate-sensitive due to its narrow thermal tolerance and recent extirpations in some warmer portions of its range. Pikas behaviorally thermoregulate by taking refuge in the subsurface microclimates found in taluses and other rocky habitats, where daily thermal fluctuations are attenuated and somewhat decoupled from free-air temperatures. Changes in microclimate might reduce the efficacy of this behavioral thermoregulation. This study compares recent (2009–2021) subsurface temperatures at a long-term pika study site with a rare instance of historical (1963–1964) data from the same location. We also place historical and recent microclimates in context using long-term data on free-air temperatures from the same area. Recent free-air temperatures were often warmer than historical records, and subsurface temperatures exhibited even stronger warming between periods. Temperatures measured in the talus were often dramatically warmer in recent records, especially at the deeper of two subsurface sensor placements in this study. Winter months showed the greatest changes in both talus and free-air temperatures. Differences between historical and recent microclimates were not explained by the precise placement of sensors, as recent temperatures were similar across a wide variety of subsurface placements, and temporal changes in free-air temperatures at the historical study site were also reflected in data from nearby weather stations. Together, these results suggest that subsurface microclimates important for pika thermoregulation have changed over the past few decades, perhaps even faster than observed changes in free-air temperatures. The generality of these results and their potential ramifications for ecosystem processes and services should be explored.