To investigate the mechanism underlying the neurodegeneration of postmenopausal women, the effect of genistein on hippocampal neurodegeneration was investigated in ovariectomized (OVX) Sprague-Dawley rats. Three-month-old female Sprague-Dawley rats were randomly divided into four groups: sham operated; OVX only; genistein-treated OVX (OVX-genistein); and estradiol benzoate-treated OVX (OVX-EB). Genistein and EB were subcutaneously injected into rats of the OVX-genistein and OVX-EB groups, respectively, once a day from the second day after surgery. Behavioral testing began on day 31 after surgery and lasted 5 d. The activities of superoxide dismutase and content of malondialdehyde in serum, the concentration of intrasynaptosome-free calcium, membrane relative viscosity of cerebral synaptosomes, and mean optical density (MOD) of the hippocampal synaptophysin immunoreactivity product were measured, respectively, in the eighth week after surgery. It was found that the escape latency in the OVX-EB and the OVX-genistein groups was significantly lower than that in the OVX control group (p < 0.05), whereas in the behavioral test, the platform-passing number was higher than in the OVX control group (p < 0.05). [Ca2+]i in the cerebral cortical and hippocampal synaptosome of the OVX-only group was remarkably higher than that in the other three groups (p < 0.01). The hippocampal synaptosome membrane viscosity of the OVX-only group was significantly higher than that in the sham-operated, OVX-EB (p < 0.05) and the OVX-genistein (p < 0.01) groups. The MOD of synaptophysin immunoreactive product in the radiation layers of CA1, CA2, CA3 and the molecular layer of the dentate gyrus of the OVX-only group was significantly lower than in the sham-operated, OVX-genistein, and OVX-EB groups (p < 0.01). These results suggested that genistein, which has antioxidant properties similar to estradiol, could be used as a substitute for estradiol to prevent or treat central neurodegeneration in postmenopausal women.