Glutathione (GSH) is an important antioxidant that plays a critical role in neuroprotection. GSH depletion in neuron induces oxidative stress promoting neuronal damage, which is regarded as a hallmark of the early stage in some neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease. The neuronal GSH levels are mainly regulated by excitatory amino acid carrier 1 (EAAC1) and its inhibitory protein, glutamate transporter-associated protein 3-18 (GTRAP3-18). In this study, we found that GTRAP3-18 levels were increased by the up-regulation of the microRNA miR-96-5p, which has been reported to decrease EAAC1 levels in our previous study. We also discovered that neuro-oncological ventral antigen 1 (NOVA1) is an intermediate protein for GTRAP3-18 expression via miR-96-5p. Moreover, we show that the intra arterial administration of a miR-96-5p-inhibiting nucleic acid to living mice by a drug delivery system using microbubbles and ultrasound decreased the levels of GTRAP3-18 via NOVA1, while increased the levels of both EAAC1 and GSH in the mouse brain. Moreover, we found that the administration of a miR-96-5p inhibitor increased autophagy activation in the mouse hippocampus. These findings suggest that the delivery of a miR-96-5p inhibitor to the brain would efficiently increase the neuroprotective activity by increasing GSH levels via EAAC1, GTRAP3-18 and NOVA1.