Phosphaturic mesenchymal tumor is an extremely rare disease and is frequently associated with oncogenic osteomalacia showing paraneoplastic syndrome, which is characterized by phosphaturia, hypophosphatemia, normocalcemia, and decreased levels of 1,25-dihydroxyvitamin D3 associated with a tumor. A 2-year-old boy, who had a soft tissue tumor on his right thigh and previously diagnosed as myositis ossificans at 9-months-old, was presented with rachitic rosary and mildly enlarged tumor. Biochemical investigations showed hypophosphatemia, hyperphosphaturia, and an increased alkaline phosphatase level of 440 U/l (25-100 U/l), suggesting rickets, which was resistant to vitamin D dietary supplementation. We were certain of intractable rickets because of oncogenic hypophosphatemia and thus decided to excise the soft tissue mass. We observed laboratory improvement of rickets after 2 weeks. On the basis of surgical and histopathological examinations, the tumor was finally diagnosed as the phosphaturic mesenchymal tumor.