Introduction: Hemophagocytic lymphohistiocytosis (HLH) is a rare condition and furthermore human immunodeficiency virus (HIV)-associated HLH is rarely reported in the literature. The most frequent presentation of secondary HLH is in association with infections, malignancies or drugs. In HIV-positive patients, the viral infection itself or the antiretroviral therapy (ART) could trigger HLH. Case presentation: A 14-year-old boy was admitted for persistent diarrhea, severe weight loss and chest burns. Laboratory tests revealed important neutropenia, which led to HIV infection diagnosis. ART in combination was started associated with granulocyte-colony stimulating factor. Viral copies declined after six weeks of treatment, but the cluster of differentiation 4 (CD4) T-lymphocytes and neutrophil counts remained very low. Infections and malignancies were ruled out. The bone marrow aspirate revealed hemophagocytosis which in association with fever, bicytopenia, hypofibrinogenemia and hypertriglyceridemia established HLH diagnosis. Cortisone therapy and intravenous immunoglobulins were added. Due to lack of response, HLH-2004 protocol was initiated in collaboration with pediatric hematologist. In the first six months of treatment, CD4 T-lymphocytes and neutrophil count remained low and then they showed significant increase simultaneously. During treatment, the patient developed spontaneous severe back pain. Magnetic resonance imaging showed vertebral compression, osteomalacia and a thoracic vertebral fracture. Conclusions: Having ruled out the usual associated infections and malignancies, this is a case of HIV-associated with HLH. In this case, only the ART and immunomodulatory therapy were not enough and failed to work. Systemic immunosuppression also worked only after a prolonged course which led to an unfortunate complication: a vertebral fracture.