A 27-year-old man with MELAS 3243 mutation developed a right homonymous hemianopia, left beating nystagmus, and impaired smooth pursuit (SP) to the left. Intermittently, the left beating nystagmus changed to right beating with rightward eye and head deviation and associated altered mental status. Each episode lasted several minutes. MRI revealed restricted diffusion in left parieto-temporo-occipital cortices. During the ictus, electroencephalogram showed epileptic discharges in the left temporo-occipital region, and single photon emission computed tomography demonstrated hyperperfusion in the same area. The interictal left beating nystagmus may be ascribed to contralesional bias of SP imbalance since the parieto-temporo-occipital region is involved in the generation of SP. The ictal right beating nystagmus and rightward head and eye deviation indicate coactivation of the SP areas and parietal eye field. This report documents the novel co-occurrence of pursuit-paretic and epileptic nystagmus.