BACKGROUND/OBJECTIVE: Epstein-Barr Virus (EBV) infection can be associated with lymphocytic hematological malignancies, including systemic Epstein-Barr virus-positive T-cell lymphoma of childhood (SEBVTCL). A common complication of EBV infection, hemophagocytic lymphohistiocytosis (HLH), is a life-threatening condition of immune activation present in virtually all cases of SEBVTCL that requires urgent treatment, as this malignancy can be rapidly fatal. Abnormal karyotypes have been strongly associated with SEBVTCL as a distinguishing feature from HLH in the literature. Here, we discuss the diagnostic challenges and social complications in the case of an unaccompanied minor immigrant patient with a highly complex karyotype diagnosed with SEBVTCL with associated HLH. METHODS: Laboratory testing confirmed the presence of EBV+ HLH and cytogenetic analysis was performed to investigate a neoplastic process in this patient, confirming SEBVTCL. Chromosomal microarray (CMA) was performed to try to clarify the complex findings by chromosome analysis but demonstrated normal results. RESULTS: Chromosome analysis demonstrated a highly complex hypertriploid clone that confirmed the diagnosis of SEBVTCL. After declining treatment, the patient was discharged to his guardian against medical advice and succumbed to his disease shortly after. CONCLUSIONS: SEBVTCL can be challenging to diagnose due to the similarity in clinical and pathological presentations. In virtually all cases reported in the literature, an abnormal karyotype has been reported to be the most important prognostic factor. We propose that in cases with diagnostic ambiguity, an abnormal karyotype can help favor SEBVTCL over EBV+ HLH.