Altricial mammals begin to independently thermoregulate during the first few weeks of postnatal development. In wild rodent populations this is also a time of high mortality (50-95%), making the physiological systems that mature during this period potential targets for selection. High altitude is a particularly challenging environment for small endotherms due to unremitting low O2 and ambient temperatures. While superior thermogenic capacities have been demonstrated in adults of some high altitude species, it is unclear if selection has occurred to survive these unique challenges early in development. We used deer mice (P. maniculatus) native to high and low altitude, and a strictly low altitude species (P. leucopus), raised under common garden conditions, to determine if postnatal onset of endothermy and maturation of BAT is affected by altitude ancestry. We found that the onset of endothermy corresponds with the maturation and activation of brown adipose tissue (BAT) at an equivalent age in low altitude natives, with 10-day old pups able to thermoregulate in response to acute cold in both species. However, the onset of endothermy in high altitude pups was substantially delayed (by ~2 days), possibly driven by delayed sympathetic regulation of BAT. We suggest that this delay may be part of an evolved cost-saving measure to allow pups to maintain growth rates under the O2-limited conditions at high altitude.