Species are shifting their ranges due to climate change, many moving to cooler and higher locations. However, with elevation increase comes oxygen decline, potentially limiting a species’ ability to track its environment depending on what mechanisms it has available to compensate for hypoxic stress. Pikas (Family Ochotonidae), cold-specialist small mammal species, are already undergoing elevational range shifts. We collected RNA samples from one population of Ochotona roylei in the western Himalaya at three sites – 3,600, 4,000, and 5,000 meters – and found no evidence of significant population genetic structure, nor any loci under positive selection between sites. However, out of over 10,000 expressed transcripts, 26 were significantly up-regulated at the 5,000 m site and were significantly enriched for pathways consistent with physiological compensation for limited oxygen. These results suggest that differences in gene expression alone may enable hypoxia tolerance on this local scale, indicating elevational flexibility that may facilitate successful range shifts in response to climate change.