Cases of dizziness caused by multiple sclerosis are commonly reported, but those caused by mitochondrial encephalomyopathy have been rarely reported. Particularly, the description of eye nystagmography (ENG) using caloric and optokinetic nystagmus tests has not been reported to date. We encountered the case of a 40-year-old woman with mitochondrial encephalomyopathy who visited us with the chief complaint of dizziness. At first, we considered multiple sclerosis based on the magnetic resonance imaging (MRI) findings and dizziness. Repeated attacks of dizziness and serum lactic acid levels suggested mitochondrial encephalomyopathy. A muscle biopsy confirmed the diagnosis. ENG findings suggested central vestibular disorder of the cerebellum and brainstem. This case suggests that we should not rule out the differential diagnosis of a very rare mitochondrial encephalomyopathy in patients who experience dizziness with MRI findings indicative of multiple sclerosis.