Complex I, the largest multisubunit enzyme complex of the respiratory chain, has a vital role in the energy production of the cell, and the clinical spectrum of complex I deficiency varies from severe lactic acidosis in infants to muscle weakness in adults. Pathogenic variants of NDUFS3 (constitutes the catalytic core of the complex I) have been reported in a small number of patients with variable phenotypes. We describe a girl with a history of infantile-onset nonepileptic myoclonus, who developed myopathy at the age of 2 years. Next-generation sequencing revealed compound heterozygous for two variants in the NDUSF3 gene. The electron-microscopic study of the skeletal muscle showed an increase in the number of mitochondria inside the myofibers; mitochondria were variably enlarged with some irregularity and were aligned perpendicular to the myofibrils in a stacked-up manner. This is the first description of mitochondrial ultrastructural abnormality in an individual with NDUFS3-related disorder.