The autopsy case of a 3-year 6-month-old boy with chordoma arising in the sacrococcygeal region is presented. The primary lesion of the sacrococcygeal area was unresectable and lung metastasis was detected. He was treated with multi-agent systemic chemotherapy and radiation therapy, but the tumor was less responsive to these therapies. He died about one year after first admission. An autopsy revealed a massive sacrococcygeal mass and metastasis in the thoracic and lumbar vertebrae, retroperitoneal and mediastinal lymph nodes, and also in the bilateral lungs and liver. Histologically, the tumor was composed of 'pink' cells and scattered 'physaliphorous' cells with a myxoid matrix. Sacrococcygeal chordoma in infancy is very rare. Our case showed a highly aggressive clinical course.