Fluoride, an environmental toxicant, could induce endoplasmic reticulum stress (ERS) in neuronal cells ultimately leading to apoptosis and emotional dysfunction. Meanwhile, voluntary wheel running contributes to mitigate anxiety and depression. Our investigation aimed to study the effect of voluntary wheel running on anxiety- and depression-like behaviors in fluoride-exposure mice. The results showed that exposure to 100 mg/L sodium fluoride (NaF) for 6 months can induce anxiety- and depression-like behavior in mice. Fluorosis mice subjected to voluntary wheel running have less anxiety- and depression-like behaviors. Nissl and TUNEL staining demonstrated that fluoride led to a reduced proportion of Nissl body area in the cerebral cortex and an increased apoptotic ratio of nerve cells in the cerebral cortex. In contrast, these pathologic damages were improved in voluntary wheel running mice exposed to NaF. Moreover, the expressions of mRNA in the cerebral cortex GABA, GAD65, GAD67, DR, vGLU, 5-HT1A, BDNF, NMDAR1, and Bcl2 were downregulated and the levels of c-fos, GRP78, PERK, eIF2α, CHOP, Caspase-12, and Caspase-3 mRNA were upregulated in mice exposed to fluoride. NaF treatment had increased the PERK, ATF6, IRE1, p-eIF2α, and Caspase-3 protein levels and reduced the expressions of proteins, including GAD67, VGAT, BDNF, NMDAR1, PSD95, and SYN. By contrast, fluorosis mice subjected to voluntary wheel running enhanced the expression of GAD65, GAD67, VGAT, and neuroplasticity-related proteins in mice and inhibited the PERK-CHOP pathway. It is worth noting that the correlation between the amount of exercise and the behavioral indicators as well as neurotransmitter levels was found. In conclusion, voluntary wheel running inhibits the fluoride-induced ERS and GRP78 expression through the PERK-CHOP pathway and plays an anti-apoptotic role, ultimately ameliorating emotional dysfunction in NaF-exposed mice.