Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH) with central nervous system (CNS) involvement is usually fatal unless stem cell transplant (SCT) is offered. However, SCT with conventional intensity conditioning is associated with high transplant-related mortality. We describe our experience with unrelated SCTs after reduced-intensity conditioning (RIC) for patients with EBV-HLH with progressive CNS disease. This approach was associated with minimal toxicities and might be an effective option in patients with EBV-HLH with progressive CNS disease. Moreover, the addition of rituximab to RIC appears to be safe and effective in suppressing EBV in the patients with EBV-HLH.