A clinical case of a genetically confirmed diagnosis of alternating hemiplegia associated with epilepsy is presented. The combination of two types of seizures in a child made it difficult to make a diagnosis. The result of video-EEG monitoring made it possible to understand that a child showed both epileptic seizures and non-epileptic seizures simultaneously with different periodicities. The mutation in the ATP1A3 gene was verified with genome-wide sequencing and targeted therapy was prescribed in a timely manner. As a result, both types of seizures stopped after treatment.