Hemophagocytic lymphohistiocytosis (HLH) is a rare heterogeneous group of disorders characterized by immune overactivation. It can occur because of primary genetic mutations or secondary to almost any inflammatory or infectious process. The clinical manifestations of this syndrome are varied and life-threatening and resemble those of many malignancies, infections, sepsis, and multisystem inflammatory syndrome in children. Laboratory abnormalities often are not diagnostic for HLH until late in the disease course, and the laboratory studies are send-out tests at most institutions. Thus, quickly and accurately diagnosing pediatric patients with HLH presents significant challenges to the clinician. Furthermore, there has been recent discussion in the literature regarding the use of diagnostic criteria for HLH. In this case report, we detail an adolescent male individual who developed persistent unexplained fever, rhabdomyolysis, and regional ischemic immune myopathy. To our knowledge, there is no previous report of a pediatric patient with this rare myopathy or HLH presenting with persistent rhabdomyolysis in the literature. The patient was hospitalized for a total of 61 days, with multiple treatments attempted throughout during his course of illness. In this report, we highlight the importance of using diagnostic flexibility when HLH is suspected in pediatric patients and provide insight into the unique challenges of identifying this condition.