Introduction: Long QT syndrome accompanied by a seizure episode is often misdiagnosed as primary epilepsy. Although patients with Long QT syndrome who are misdiagnosed and improperly managed are likely to result in fatality, their first clinical manifestations are seizure episodes in many cases. Case presentation: A 17-year-old boy visited the emergency department with poorly controlled seizure during epilepsy treatment was found to have been misdiagnosed with epilepsy when he was 7 years old. His electrocardiography showed a prolonged QT interval. After careful re-evaluation, he was finally diagnosed with Long QT syndrome and recovered without any seizure episodes in the absence of anti-epileptic agents. Discussion and conclusion: Careful initial assessment including repetitive electrocardiography, when abnormal, is required for those who visit the emergency department with a seizure or who show no definite abnormalities in diagnostic work up process.