Background: The neurite extension and migration factor (NEXMIF) gene encodes the neurite growth-directed factor whose main function is to play a role in neurite extension and migration for nerve development. It is associated with X-linked intellectual disability 98 and X-linked dominant inheritance, and its clinical manifestations mainly include intellectual disability, autistic behavior, poor development, dysmorphic features, gastroesophageal reflux, renal infection, and early seizures. Few cases of patients with NEXMIF variants had been reported, and to date, no deaths have been reported to our knowledge. Case Description: We present a clinical report of a female child who had a history of epilepsy, and was diagnosed with multiple organ failure (MOF), sepsis, hemophagocytic lymphohistiocytosis, severe pneumonia, and pulmonary hemorrhaging. Genetic testing identified the NEXMIF variant c.937C>T (p.R313*) in this patient. Despite aggressive treatment with anti-inflammation drugs with methylprednisolone, plasma exchange, hemodialysis and mechanical ventilation, the patient died. Conclusions: We reported the first case of the NEXMIF variant in a patient with the symptom of MOF, including acute liver failure and acute kidney injury (Grade 3). In addition, some complications, such as sepsis, hemophagocytic syndrome, pneumonia, and pulmonary hemorrhage, can also occur with this disease. All of these complications may have contributed to the patient's death. This report not only broadens the phenotype for NEXMIF variants but may also help physicians involved in the care of patients with this syndrome and enhance their understanding of this variant.