Objective To investigate the protective effect of ginkgolide A and ginkgolide B (GKAB) mixture on neurons of rats with permanent middle cerebral artery occlusion (pMCAO) and related molecular mechanisms. Methods Sixty male Sprague-Dawley rats were randomly divided into sham group, pMCAO permanent focal cerebral ischemia group and GKAB-treated low-, medium- and high-dose groups. In addition to the sham group (only isolated without interruption of the arteries), the rats in the remaining four groups were induced pMCAO by blocking the right middle cerebral artery. Rats in the GKAB-treated low-, medium- and high-dose groups were injected with GKAB 12.5, 25, and 50 mg/kg through sublingual vein at 10 min after pMCAO, while the sham and pMCAO groups were injected with saline of the same volume as the medium-dose group. After 12 h of treatment, the neuronal apoptosis was determined by TUNEL method, the level of phosphorylated c-Jun N-terminal kinase (p-JNK) was determined by immunohistochemistry, the expressions of p-JNK, Bcl-2, Bax, cytochrome C (Cyt C), caspase-9, caspase-3, cleaved caspase-9, and cleaved caspase-3 in brain tissues were detected by Western blotting. Results Compared with the sham group, the apoptosis rate and p-JNK expression of neurons in the pMCAO group were significantly increased (P<0.01), and the expressions of apoptosis-related proteins Bax, cleaved caspase-9 and cleaved caspase-3 in brain tissues were significantly increased (P<0.01), while the expressions of Bcl-2, caspase-9 and caspase-3 in brain tissues were significantly decreased (P<0.01). Compared with the pMCAO group, the apoptosis rate and p-JNK expression of neurons in GKAB-treated low-, medium- and high-dose groups were significantly decreased (P<0.01), the expressions of Bax, cleaved caspase-9 and cleaved caspase-3 protein were significantly decreased (P<0.01), and the expressions of Bcl-2, caspase-9 and caspase-3 were significantly increased (P<0.01) in a dose-dependent manner. Compared with the sham group, the expression of Cyt C in cytoplasm in the pMCAO group was significantly increased, and the expression of mitochondrial Cyt C was significantly decreased (P<0.01). Compared with the pMCAO group, the expressions of Cyt C in cytoplasm in the GKAB-treated low-, medium- and high-dose groups were significantly decreased in a dose-dependent manner, and the expressions of mitochondrial Cyt C were significantly increased (P<0.05, P<0.01). Conclusion GKAB can inhibit neuronal apoptosis after pMCAO in rats, and its mechanism may be related to the inhibition of JNK phosphorylation and JNK signaling pathway and the block of mitochondrial apoptosis pathway.