Background A 27-year-old male with perinatal hypoxia presented with global developmental delay, progressive hearing loss, ataxia, dysarthria, and intellectual disability. Whole-exome sequencing revealed compound heterozygous ACAD9 variants: c.456del (p.Ile153Serfs*46) and c.869G > A (p.Gly290Glu). Brain MRI showed bilateral cerebellar atrophy and a prominent cisterna magna. OCT confirmed optic atrophy. The diagnosis of mitochondrial encephalomyopathy (complex I deficiency type 20) was established. This report expands the known genetic spectrum associated with mitochondrial encephalomyopathy and underscores the critical role of genomic sequencing in diagnosing atypical, slowly progressive multisystem disorders.