Background Widespread alveolar rhabdomyosarcoma (ARMS) with bone marrow involvement and with an unknown primary tumor, especially presenting with acute tumor lysis syndrome can be easily misdiagnosed as a hematological malignancy. Furthermore, brain metastasis of ARMS is rare seen in children. Case report Herein, we report a 14-year-old boy presenting with acute tumor lysis syndrome due to bone marrow invasion of ARMS, who was diagnosed after abdominal paraaortic lymph node biopsy. Despite radiological and nuclear medicine imaging, the primary tumor site could not be found. He was treated with vincristine, topotecan, and cyclophosphamide for 42 weeks. Six months after the completion of treatment, he suffered from severe headache, blurred vision, right hemiplegia, and severe bone pain. Cranial magnetic resonance imaging showed multiple hemorrhagic infarctions. Brain biopsy showed brain metastasis with PAX3-FKHR fusion transcript. Conclusion The clinicians must be vigilant about solely brain metastasis in ARMS without additional metastasis.