Here, we isolated Drosophila Nardilysin (NRD1) (dNrd1) from a forward genetic screen designed for identification of genes whose loss causes neurodevelopmental or neurodegenerative phenotypes. We show that NRD1 is localized to the mitochondria whereas previous reports have documented a cytosolic, nuclear and plasma membrane localization. Unlike other mitochondrial mutants isolated from the screen, loss of dNrd1 mutants did not affect reactive oxygen species, and ATP production, or mitochondrial contents. Rather, metabolomic studies and enzymatic assays revealed that dNrd1 mutants exhibit a striking defect in α-Ketoglutarate Dehydrogenase (OGDH), a rate-limiting enzyme in Krebs cycle. To define the function of NRD1, we performed IP-mass spec and identified OGDH as well as numerous mitochondrial chaperones as NRD1-binding partners. Based on biochemical assays, we showed that NRD1 acts in a mitochondrial chaperoning complex to fold OGDH. Moreover, we show that loss of OGDH phenocopied the loss of NRD1, suggesting that OGDH is a major target of NRD1. A decreased OGDH activity in NRD1 mutants or OGDH knockdown animas caused an increase in α-ketoglutarate, and glutamine levels, which in turn leads to mTORC1 activation, and inhibition of autophagy, resulting in a progressive neurodegeneration. Inhibition of mTOR activity by rapamycin delays the neurodegeneration phenotype in dNrd1 mutant or OGDH knockdown flies. Furthermore, we describe the identification of two patients with rare variants in NRD1 or OGDH-like (OGDHL) who exhibit a progressive neurodegeneration with an acquired microcephaly and ataxia. Using state of the art technology in Drosophila, we demonstrated that the variant in OGDHL in the patient is pathogenic. The cross-species functional studies described here reveal a novel role for NRD1 as a mitochondrial chaperone for OGDH, foster the discovery of two novel human diseases, and provide a potential therapeutic strategy.