Abstract: Hematopoietic stem cell transplantation (HSCT) patients may develop cytomegalovirus encephalitis, a rare but life-threatening complication with a mortality rate exceeding 90%. Cytomegalovirus encephalitis is rare and does not have specific clinical manifestations, which makes clinical diagnosis more difficult. This article reports a pediatric case of acute lymphoblastic leukemia (ALL) with early onset (81 d after transplantation) cytomegalovirus encephalitis after HSCT, with palpitations presenting as the initial symptom. The patient exhibited rapid clinical progression and the treatment was ineffective. This case report can help clinicians gain further understanding of the high-risk factors and clinical features of central nervous system complications following HSCT. When encountering unexplained tachycardia, clinicians should still be vigilant for the possibility of intracranial infection even in the absence of typical neurological manifestations associated with encephalitis. Early recognition and management may help improve the outcomes of such patients.