Background: NADH dehydrogenase 5 (ND5) is one of 44 subunits forming Complex I in the mitochondrial respiratory chain. Therefore, a mitochondrially encoded ND5 (MT-ND5) gene mutation causes mitochondrial oxidative phosphorylation (OXPHOS) disorder, resulting in the development of mitochondrial diseases, such as mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. Although focal segmental glomerulosclerosis (FSGS) is induced by several mitochondrial diseases, no reports have yet confirmed that an MT-ND5 mutation causes FSGS. Case presentation: A Japanese woman at 29 years old was found to have proteinuria and renal dysfunction in an annual health check-up for the first time. Because her proteinuria and renal dysfunction were persistent, she was admitted for a kidney biopsy to investigate the reason at 33 years of age. Although there were no abnormal neurological findings, she was diagnosed with sensorineural hearing loss by an otolaryngologist. Renal histology showed perihilar variant-type FSGS with podocytes filled with abnormal mitochondria. In addition, the renal pathological findings showed granular swollen epithelial cells (GSECs) in tubular cells, age-inappropriately disarranged and irregularly sized vascular smooth muscle cells (AiDIVs), and red-colored podocytes (ReCPos) by acidic dye, which are assumed to be characteristic changes of mitochondrial nephropathy. Genetic analysis using peripheral mononuclear blood cells and urine sediment cells detected the m.13513 G>A variant, which has already been confirmed as a pathogenic variant of the MT-ND5 gene. The heteroplasmy rates of the blood cells and urine sediments were 10.3% and 62.2%, respectively. Therefore, this patient was diagnosed with FSGS due to an MT-ND5 mutation. Conclusion: This is the first case report to show that a gene mutation encoding subunits of Complex I causes FSGS with podocytes filled with abnormal mitochondria. The routine evaluation of GSECs, AiDIVs, and ReCPos is expected to be useful for detecting mitochondrial nephropathies, which could be latent in etiology-unknown FSGS or glomerulosclerosis cases.