We reported a 10-year-old male with vacuolating leukoencephalopathy with subcortical cysts, who presented athetotic movements in the late stage. Magnetic resonance imaging demonstrated diffuse cerebellar white matter lesions, in addition to typical cerebral white matter abnormalities and characteristic subcortical cysts in the anterotemporal and parietal areas. Fluid-attenuated inversion recovery images are highly sensitive for the detection of subcortical cysts, which is essential for a diagnosis. This is most likely to be a severe form of vacuolating leukoencephalopathy with subcortical cysts, presenting with athetotic movements in the late stage.