Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening condition that often goes underdiagnosed because of broad and non-specific symptomatology, usually consisting of fever, hepatosplenomegaly, and multiorgan failure. This disorder can be driven by genetic components (primary) or acquired (secondary) causes related to infectious, autoimmune, or malignant processes. HLH pathogenesis derives from overactive and dysregulated immune system responses. This disorder often goes misdiagnosed because of similar clinical and laboratory findings to septicemia. Cases of HLH most commonly coexist with Epstein-Barr virus (EBV). Clostridium difficile (C. difficile) infection causing HLH has also rarely been described in the literature. A firm knowledge of HLH association with clostridial infection is essential to recognize. A presumed diagnosis of HLH in a decompensating patient may prompt the initiation of appropriate treatment earlier and improve clinical outcomes. We discuss the diagnostic and management difficulties associated with these concurrent conditions.