This study was conducted to further explore the effect of selenium on fluoride-induced changes in the synaptic plasticity in rat hippocampus. Animals were randomly divided into control group, F group (sodium fluoride: 50 mg/L), three Se groups (sodium selenite: 0.375, 0.75, and 1.5 mg/L), and three F?+?Se groups (sodium fluoride: 50 mg/L; sodium selenite: 0.375, 0.75, and 1.5 mg/L) and subjected to an exposure time of 6 months. The changes in synaptic plasticity in rat hippocampus were observed by electron microscopy. Compared with the fluoride group, the length of the synaptic active zone and the thickness of the postsynaptic density (PSD) increased significantly, whereas the width of the synaptic cleft decreased with high significance in the F?+?Se (0.75 mg/L) group. Moreover, the nitric oxide synthase activity and the nitric oxide content in the hippocampus decreased significantly in the F?+?Se (0.75 and 1.5 mg/L) groups. Furthermore, reverse transcriptase polymerase chain reaction and Western blot analyses showed that postsynaptic density-93 (PSD-93) expression in the hippocampus was increased significantly, whereas postsynaptic density-95 (PSD-95) expression decreased significantly in the fluoride group compared with the control group. The PSD-93 expression was inhibited in the three F?+?Se groups, whereas the opposite result was observed in PSD-95 expression. Based on the results, the optimal selenium dosage range that can antagonize the neurotoxicity of fluorosis is from 0.75 to 1.5 mg/L. The changes in PSD-93 expression may be the key factor to fluoride-induced central nervous toxicity and the effect of selenium intervention.