Ginkgolide B (GB) is one of the ginkgolides isolated from leaves of the Ginkgo biloba tree. The aim of this study was to investigate whether GB has a protective effect on high altitude cerebral edema (HACE) of rats. HACE was induced by hypobaric hypoxia exposure for 24 hours in an animal decompression chamber with the chamber pressure of 267 mmHg to simulate an altitude of 8000 m. Before the exposure, three doses (3, 6, and 12 mg·kg(-1)) of GB were given intraperitoneally (ip) daily for 3 days. Effects of GB on brain water content (BWC), activity of superoxide dismutase (SOD), concentration of glutathione (GSH) and malondialdehyde (MDA), expression of active caspase-3 and poly(ADP-ribose) polymerase (PARP) were measured. In GB pretreatment groups (6 and 12 mg·kg(-1), but not 3 mg·kg(-1)), BWC, the concentration of MDA, the expression of active caspase-3 and PARP were reduced significantly, while the activity of SOD and concentration of GSH were significantly increased. In conclusion, these results indicate that GB has a protective effect on cerebral edema caused by high altitude in rats. The protective effect of GB might be attributed to its antioxidant properties and suppression of the caspase-dependent apoptosis pathway.