Objective To investigate the protective function and mechanism of rapamycin on the hypothalamus injury of rats with exertional heat stroke. Methods Eighty male Wistar rats were randomly divided into four groups: control group, rapamycin group (Rapa group), exertional heat stroke group (EHS group), and exertional heat stroke + rapamycin group (EHS+Rapa group), with 20 rats in each group. The rats in Rapa group and EHS+Rapa group were injected intraperitoneally with Rapa (1 mg/kg, once a day) for four consecutive days before modeling. The rats in control and EHS groups were treated with the same dose of 0.9% normal saline. In EHS group and EHS+Rapa group, the rats ran in a climate chamber with a temperature range of (39.5±0.3) ℃ and a humidity range of (55%±5%). After successful modeling, the rats were removed from the climate chamber for cooling at room temperature. The animals in control and Rapa groups ran at the same intensity and room temperature as EHS group. During the establishment of the model, we monitored the general state, measured core temperature, and profiled the survival curve of the rats in each group (11 rats randomly selected from each group). The rats in EHS group and EHS+Rapa group were removed from the chamber after modeling of 80 min, and after 300 min observation, each group of rats was anesthetized. Then we collected the abdominal aorta blood and hypothalamus. The histopathological changes in the hypothalamus were analyzed by HE and Nissl staining. Immunofluorescence was used to determine the apoptosis of hypothalamus. Western blotting was used to detect the expression of mammalian target of rapamycin (mTOR) and phosphorylated mTOR (pmTOR), autophagy effector protein (Beclin-1), ubiquitin-binding protein (p62) and autophagy marker microtubule-associated protein 1 light chain 3(LC3) in the hypothalamus of rats. We calculated the ratios of pmTOR/mTOR and LC3-Ⅱ/LC3-Ⅰ. We measured the expression levels of neuron-specific enolase (NSE), brain active peptide 100β protein (S100β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) in arterial serum by ELISA. Results When rats were entered into the climate chamber at 80 min, compared with control group, the core temperature of EHS group was significantly increased (P<0.001); compared with Rapa group, the core temperature of EHS+Rapa group was significantly increased (P<0.001). Compared with the EHS group, the survival rate of EHS+Rapa group was increased (P<0.01). HE and Nissl staining showed severe pathological damage in hypothalamic nerve cells in EHS group. We observed significantly less pathological damage in hypothalamic nerve cells in EHS+Rapa group than EHS group (P<0.001). Immunofluorescence analysis showed substantial cell apoptosis in the hypothalamus of EHS rats compared with control group (P<0.05). EHS+Rapa group had significantly less apoptosis in the hypothalamus than EHS group (P<0.05). Western blotting results showed that compared with control group, the ratio of pmTOR/mTOR, Beclin-1 expression, LC3-Ⅱ/LC3-Ⅰ ratio in the hypothalamus tissue of EHS group increased and p62 expression decreased (P<0.01); compared with EHS group, the ratio of pmTOR/mTOR in the hypothalamus of EHS+Rapa group decreased, Beclin-1 expression increased, LC3-Ⅱ/LC3-Ⅰ ratio increased and p62 expression decreased (P<0.05). ELISA results showed that the expression levels of NSE, S100β protein, and TNF-α in the serum of EHS group were significantly increased (P<0.05), while the expression of IL-6 in EHS group showed no significant difference (P>0.05). Compared with EHS group, the expression levels of NSE, S100β protein, IL-6, and TNF-α in the serum of EHS+Rapa group were significantly decreased (P<0.05). Conclusion Rapa can alleviate the hypothalamus tissue damage caused by exertional heat stroke, improve the function of brain cells, reduce the levels of inflammatory factors and the apoptosis of tissue cells, which is related to the inhibition of mTOR signaling pathway and the enhancement of hypothalamus autophagy level.