Background Primary amebic meningoencephalitis is a rare, almost uniformly fatal disease of cerebral invasion by Naegleria fowleri, occurring most commonly after swimming in warm fresh water in summer months. Treatment using the experimental medication miltefosine demonstrated improved survival and favorable neurocognitive outcome in a 2013 North American patient. There is little information about the electroencephalographic findings of such patients, and our understanding of factors predicting survival is limited. Methods and Results We describe two children, aged four and 14 years, who both presented with seizures and altered mental status after recent fresh water swimming exposures. With evidence of pyogenic meningitis and examination of cerebrospinal fluid demonstrating motile trophozoites on wet mount, N. fowleri meningoencephalitis was diagnosed. Amebicidal antibiotic regimens with miltefosine were administered. Continuous electroencephalography monitoring demonstrated evolution from diffuse slowing to seizures, status epilepticus, and eventually global attenuation and absence of activity. Both patients ultimately died after complications of progressive increasing intracranial pressure and hemodynamic compromise. Conclusions Primary amebic meningoencephalitis is a serious, sporadic infection. We describe two fatal pediatric patients, the evolution of their electroencephalography findings, and compare their findings with the 13 reported pediatric survivors.