Familial hemophagocytic lymphohistiocytosis (FHL) is a fatal disease of early infancy caused by defective natural killer cell activity and is characterized by fever, organomegaly, pancytopenia, and coagulopathy. Disease-causing mutations have been found in perforin, Munc 13-4 and syntaxin-11 genes. We herein describe a case of late-onset FHL with syntaxin-11 mutation in a six-year-old boy in whom only partial response was obtained by immunochemotherapy (HLH-94 protocol) and who died with persistent Epstein-Barr virus (EBV) infection. The role of EBV infection in the prognosis of FHL is discussed.