We report a case of primary alveolar rhabdomyosarcoma of the breast in a 13-year-old Japanese girl. The patient initially presented with a 13 × 8-cm mass in her left breast, which was diagnosed as alveolar rhabdomyosarcoma after an excisional biopsy. Genetic expression of the tumor revealed t(2;13)(q35–37;q14). She underwent modified radical mastectomy (Bt + Ax) and nine lymph nodes were found to be involved. Systemic examinations showed multiple bone and lung metastases 2 weeks after her operation. Despite chemotherapy with doxorubicin, ifosfamide, and actinomycin D, which resulted in remission for 6 months, she died of the disease 8 months after surgery.