Reports have showed that Sigma-1 receptor (Sig-1R) activation can protect neurons against cerebral ischemia/reperfusion (I/R) injury in mice and alleviate endoplasmic reticulum (ER) stress in cultured cells, but little known is about the protective role of Sig-1R on ER stress induced by cerebral I/R. The purpose of this study was to determine whether Sig-1R exerts a protective effect against ER stress-mediated apoptosis in cerebral I/R using a 15-min bilateral common carotid artery occlusion (BCCAO) mouse model. At 72 h after reperfusion in BCCAO mice, we found that Sig-1R knockout (Sig-1R KO) significantly increased terminal dUTP nick-end labeling (TUNEL)-positive cells and nuclear structural damage in cortical neurons. Treatment with the Sig-1R agonist PRE084 once daily for three consecutive days reduced the number of TUNEL-positive cells and improved the ultrastructural damage of neurons in the cerebral cortex. These protective effects could be blocked by the Sig-1R antagonist BD1047. Then, we used BCCAO mice at 24 h after reperfusion to detect the expression of ER stress-mediated apoptotic pathway proteins. We found that expression of the pro-apoptotic proteins p-PERK, p-eIF2α, ATF, CHOP, p-IRE, p-JNK, Bim, PUMA, cleaved-caspase-12 and cleaved-caspase-3 was significantly increased and that expression of the anti-apoptotic protein Bcl-2 was significantly decreased in Sig-1R KO-BCCAO mice compared with BCCAO mice. Meanwhile, we found that treatment with PRE084 twice a day decreased pro-apoptotic protein expression and increased anti-apoptotic protein expression. The effects of PRE084 were blocked by the Sig-1R antagonist BD1047. These results suggest that Sig-1R activation inhibits ER stress-mediated apoptosis in BCCAO mice, indicating that Sig-1R may be a therapeutic target for neuroprotection particularly relevant to ER stress-induced apoptosis after cerebral I/R injury.