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This study investigated whether crocin exerted neuroprotective effects against acute hypobaric hypoxia at high altitude in vivo and determined the underlying mechanisms. Male Sprague-Dawley rats were randomly assigned to a normoxic group, a hypoxic group, and three crocin groups at three different doses. The rats were transferred from 50 m to 4200 m for 3 days after treatment with crocin for 3 days. The learning and memory of the rat were evaluated with the Morris water maze test. Transmission electron microscope (TEM) was used to analyze the changes in the ultrastructure of hippocampal neurons. Peroxisome proliferator-activated receptor-γ co-activator 1α (PGC-1α) and sirtuin-1 (SIRT1) levels were determined using immunohistochemical staining and western blotting. The escape latency of the crocin group was shorter than that of the hypoxic group, while the frequency of the rats reaching the platform was significantly higher in the crocin group. The structures of nerve cells and mitochondria were destroyed in the hypoxic group, but were repaired in the crocin groups. The expressions of PGC-1α and SIRT1 were decreased in the hypoxic group, but were increased in the crocin group. All the effects improved by crocin were dose-dependent. Crocin attenuates acute hypobaric hypoxia-induced cognitive deficits in rats, accompanied by repairing the structures of hippocampal neurons and improving PGC-1α and SIRT1 levels.