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Ginkgo biloba flower extract (GBF) is the extract of Gymnosperm Ginkgo biloba male flower rich in active ingredients. The present study was conducted to investigate the potential preventive and therapeutic effects of GBF on brain injury caused by microwave radiation in rats. The experimental results demonstrated that GBF can significantly shorten the average escape latency (AEL) of irradiated rats and so effectively improve brain spatial learning and memory dysfunction caused by microwave radiation in rats. Furthermore, it was observed that GBF can improve abnormal blood routine: white blood cell (WBC), lymphocyte (LYM), lymphocyte percentage (LYM%), neutrophil percentage (NEU%), as well as hemoglobin (HGB), and alleviate the disorder of blood biochemistry: the glutamic oxalacetic transaminase (AST), creatine kinase (CK), triglyceride (TG), and lactic dehydrogenase (LDH). After GBF treatment, 13 kinds of abnormal lipid metabolites covered phosphatidylcholines (PCs), sphingomyelins (SMs), and triglycerides (TGs) caused by microwave radiation were significantly regulated. Our study will provide a scientific basis for the development of a new anti-microwave agent targeting cerebral protection.