Glutamate is the most abundant excitatory neurotransmitter in the vertebrate central nerve system and plays an important role in synaptic plasticity required for learning and memory. Activation of glutamate ionotropic receptors promptly triggers membrane depolarization and Ca2+ influx, resulting in the activation of several different protein kinases and transcription factors. For example, glutamate-mediated Ca2+ influx activates Ca2+/calmodulin-dependent kinase, protein kinase C, and mitogen activated protein kinases resulting in activation of transcription factors such as cyclic AMP response element binding protein (CREB). Abnormally prolonged exposure to glutamate causes neuronal injury, and such “excitotoxicity” has been implicated in many acute and chronic diseases including ischemic stroke, hypoglycemia, epilepsy, amyotrophic lateral sclerosis, Alzheimer’s, Huntington’s and Parkinson’s diseases. Interestingly, although glutamate-induced Ca2+ influx can cause DNA damage by a mitochondrial reactive oxygen species-mediated mechanism, the Ca2+ simultaneously activates CREB, resulting in up-regulation of the DNA repair and redox protein apurinic/apyrimidinic endonuclease 1. Here, we review connections between physiological or aberrant glutamate receptor activation, Ca2+-mediated signaling, oxidative DNA damage and repair efficiency, and neuronal vulnerability. We conclude that glutamate signaling involves an adaptive cellular stress response pathway that enhances DNA repair capability, thereby protecting neurons against injury and disease.