Alternating hemiplegia of childhood (AHC) is a distinct clinical disorder characterized by recurrent episodes of hemiplegia, abnormal ocular movement, and progressive developmental delay. It is an extremely rare genetic disorder related to ATP1A3 gene mutations. In this paper, we present a case of AHC in which the diagnosis was missed for many years until severe hypoxic brain insult occurred from prolonged status epilepticus. Not only we are presenting an interesting clinical entity and radiological images, but also we are shedding the light on a rare genetic disease with catastrophic sequelae. The challenges in diagnosis and treatment lead to a poor outcome as seen in our case. Although early recognition and accurate diagnosis and treatment of the disease may not change the outcome, counseling of the family may change their expectation and reduce their frustration. Referral to a center with expertise in genetic disorders and access to genetic laboratories is of paramount importance in the diagnosis of this disease. Due to the rarity of this disease in Saudi Arabia, a genotype-phenotype correlation is not feasible.