We describe herein a rare case of primary rhabdomyosarcoma (RMS) occurring in the sacrum. A 16-year-old woman presented with a 2-month history of pain in bilateral buttocks and posterior thighs. Computed tomography showed a primary tumor with bone destruction in the 2nd sacral vertebra and invasion to the 1st to 3rd vertebrae and retroperitoneal space. Histological examination of the tumor showed proliferation of spindle-shaped cells intermingled with rhabdomyoblasts in a fascicular and storiform growth pattern. Tumor cells showed immunoreactivity for vimentin, desmin, muscle-specific actin, sarcomeric actin, α-smooth muscle actin and CD99, and partial immunoreactivity for myoD1, myf-4, myogenin and myoglobin. Reverse transcription polymerase chain reaction demonstrated expression of myoD1. On the basis of the aforementioned findings, a poorly differentiated spindle cell variant of embryonal RMS was diagnosed. The patient underwent combined therapy with chemotherapy and radiotherapy, but died 17 months after incisional biopsy. The present case is instructive in differential diagnosis of primary bone tumors, and the possibility of skeletal RMS needs to be considered.