A 15-year-old boy with fever, pancytopenia, and hepatosplenomegaly was diagnosed as hemophagocytic lymphohistiocytosis (HLH). 18F-FDG PET/CT showed hypermetabolic foci in the liver, spleen, and bone marrow, as well as multiple FDG-avid lymph nodes, which were highly suggestive of lymphoma. Specimens from splenectomy depicted a large number of macrophages/histiocytes with hemophagocytosis of erythrocytes, without evidence of malignancy. Considering increased Epstein-Barr virus (EBV) DNA in peripheral blood and positive staining for EBV-encoded RNA in the spleen, EBV-associated HLH was confirmed. This case indicates that FDG-avid foci in the liver, spleen, and bone marrow may also be seen in EBV-associated HLH.