Hypothermia and frostbite are frequently seen in accidents in remote wilderness environment, especially in hypobaric hypoxic conditions. The aim of this study was to clarify how hypobaric hypoxic conditions affects peripheral circulation. Peripheral skin temperature and autonomic nervous functions were assessed in two 1000-m ascent exercises. Subjects (n = 15) ascended from 1000 m above sea level in Study 1, and ascended from 2400 m in Study 2. Conditions other than environmental oxygen pressure were mostly identical in both studies. The autonomic nervous activities were decreased solely in Study 2. The relative sympathetic activity was significantly increased in the lower barometric pressure in Study 2 (p < 0.01). Peripheral skin temperature was significantly decreased after the exercise in Study 2 (p < 0.01). In conclusion, hypobaric hypoxia itself induced peripheral low temperature during exercise at high altitudes. Relative sympathetic hyperactivity may be responsible for the compromised peripheral circulation.