Background: The outcome of extramedullary infiltration (EMI) in pediatric acute myeloid leukemia (AML) is controversial, and little is known about the implications of stem cell transplantation (SCT) and gemtuzumab ozogamicin (GO) treatment on AML patients with EMI. Methods: We retrieved the clinical data of 713 pediatric AML patients from the TARGET dataset and analyzed the clinical and prognostic characteristics of patients with EMI at initial diagnosis and relapse. Results: A total of 123 patients were identified to have EMI at initial diagnosis and 64 presented with EMI at relapse. We discovered that the presence of EMI was associated with age ≤2 years, M5 morphology, abnormal karyotype, and KMT2A rearrangements. Hyperleukocytosis and complex karyotype were more prevalent in EMI relapse patients. Additionally, patients with EMI at diagnosis showed a reduced incidence of FLT3 ITD-/NPM1+, whereas EMI relapse patients displayed a lower frequency of FLT3 ITD+. Patients with EMI at diagnosis exhibited a lower rate of CR1 and higher incidence of relapse. Importantly, EMI at diagnosis independently predicted both shorter EFS and OS. Regarding relapse patients, the occurrence of EMI at relapse showed no impact on OS. However, relapse patients with myeloid sarcoma exhibited a poorer OS compared to those with exclusive CNS involvement. Furthermore, in reference to patients with EMI at initial diagnosis, SCT failed to improve the survival, whereas GO treatment may potentially enhance OS. Conclusion: EMI at initial diagnosis is an independent prognostic risk factor, GO treatment has the potential to improve survival for patients with EMI at diagnosis.