The aim of this study was to investigate the antioxidant and anti-apoptotic activities, as well as the underlying mechanisms of action, of Scrophularia buergeriana ( S. buergeriana) extract (SBE) in glutamate-induced SH-SY5Y cell death. The roots of S. buergeriana were extracted with 70% ethanol, and standardized SBE was used in this study. To induce cytotoxicity, the SH-SY5Y cells were exposed to glutamate for 3 h, or pre-treated with SBE for 1 h, and subsequently incubated with glutamate for 3 h. The neuro-protective effects were assessed by measuring cell viability and the total glutathione contents using commercial kits. The antioxidant and anti-apoptotic mechanisms of action of SBE were evaluated by western blot analysis. The results confirmed that glutamate-induced toxicity was caused by reactive oxygen species (ROS) production, leading to oxidative stress and DNA damage, thus leading to cell death. However, treatment of the SH-SY5Y cells with SBE significantly increased the viability of the cells exposed to glutamate by upregulating the levels of antioxidant proteins, such as superoxide dismutase (SOD)1, SOD2 and glutathione peroxidase-1 (GPx-1), and directly enhancing the total glutathione contents. Furthermore, SBE attenuated DNA impairment and decreased B-cell lymphoma-2 (Bcl-2)-associated X protein (Bax), cleaved caspase-3 and cleaved poly(adenosine diphosphate (ADP)-ribose) polymerase (PARP) activation. In addition, SBE upregulated Bcl-2 expression via p38 mitogen-activated protein kinases (MAPKs). On the whole, the findings of this study demonstrated that SBE exerts neuroprotective effects against glutamate-induced cell toxicity through its antioxidant and anti-apoptotic activities.