Necrostatin-1 (Nec-1) has previously been shown to protect neurons from death in traumatic and ischemic brain injuries. This study tests the hypothesis that Nec-1 protects neural cells against traumatic and ischemic brain injuries through inhibition of the Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (BNIP3). We have used biochemical and morphological techniques to determine the inhibition of Nec-1 on BNIP3-induced cell death and to identify its mechanism of action in in vivo and in vitro models of neurodegeneration. Here we show that Nec-1 significantly increased neuronal viability following prolonged exposure to hypoxia in vitro, and attenuated myelin damage and neuronal death in traumatic brain injury and cerebral ischemia in Sprague-Dawley rats. Nec-1 alleviated traumatic brain injury-induced up-regulation of BNIP3 in mature oligodendrocytes. In isolated mitochondria, Nec-1 prevented BNIP3 from integrating into mitochondria by modifying its binding sites on the mitochondria. Consequently, Nec-1 robustly inhibited BNIP3-induced collapse of mitochondrial membrane potential and reduced the opening probability of mitochondrial permeability transition pores. Nec-1 also preserved mitochondrial ultrastructure and suppressed BNIP3-induced nuclear translocation of apoptosis-inducing factor. In conclusion, Nec-1 protects neurons and oligodendrocytes against traumatic and ischemic brain injuries by targeting the BNIP3-induced cell death pathway, and is a novel inhibitor for BNIP3. Cover Image for this issue: https://doi.org/10.1111/jnc.15056.