We report an 18-year old female patient with systemic lupus erythematosus (SLE), who developed fever, pancytopenia, abdominal pain, and watery diarrhea. Computed tomography (CT) and bone marrow aspirate revealed lupus mesenteric vasculitis (LMV) and hemophagocytic syndrome (HPS). Serologic tests for Epstein-Barr virus (EBV) indicated its reactivation. This case demonstrates that HPS and concomitant LMV associated with viral reactivation can occur as clinical manifestations of SLE flare.