Neurotrophic human Astrovirus (HAstV) VA1/HMO can cause severe encephalitis in immunocompromised patients. Advanced diagnostic tools are often required for diagnosis. Previous studies have described cases of acute HAstV VA1/HMO encephalitis that developed after allogeneic hematopoietic cell transplantation (HCT) with a fatal outcome. Here, we describe a rare case of a patient that survived severe progressive HAstV VA1/HMO encephalitis following HCT. The halt in clinical deterioration coincided with recovery of lymphoid competence, which indicated that the neuroinvasive HAstV infection was controlled by the reconstituting immune system.