Radiation therapy has been known to have a prophylactic effect for heterotopic ossification (HO), but until now it has not been known to have a therapeutic effect for established HO. We report a case of established HO compounded with a sudden increase in activity, that was improved with radiation therapy. A patient with traumatic brain injury had HO in both hips and thighs two months after the initial trauma. The existing level of HO activity suddenly increased seven months after the initial trauma, and was accompanied by severe pain that was refractory to indomethacin. We assumed that the pain was caused by the increased activity of HO on the basis of clinical symptoms and laboratory results. Initially, the patient received radiation therapy to the left lower extremity, with a total dose of 20 Gy in ten fractions. Next, the patient received radiation therapy at the same dosage to the right lower extremity, after which the pain and level of serum alkaline phosphatase significantly decreased. The patient experienced a mild pancytopenia as a side effect of the radiation therapy, but it was not severe enough to stop the radiation therapy, given the patient's suffering from the increased HO activity.