A 3-month-old girl exhibited asymmetric abnormal eye movement and unilateral dystonic posture intermittently after the first few days of life. Unilateral ocular deviation or nystagmus were the main signs of abnormal eye movements. She was suspected to have alternating hemiplegia of childhood (AHC) despite the absence of apparent alternating hemiplegic episodes. Gene analysis revealed a de-novo missense mutation (Asp801Asn) of ATP1A3. AHC is a rare neurodevelopmental disorder characterized by recurrent transient attacks of hemiplegia affecting the unilateral or bilateral side of the body; in most cases, these attacks begin in the first 6 months of life. Initial symptoms of AHC are not alternating hemiplegic episodes, but rather asymmetric abnormal eye movement, dystonic posture, or seizures. It is difficult to diagnose AHC early because no specific findings are observed in the diagnostic laboratory or neuroradiological examinations. Early diagnosis is important because flunarizine may have a protective effect on the severe motor deterioration associated with AHC. Asymmetric abnormal eye movement could be an important clinical symptom for the diagnosis of AHC in early infancy.