Osteoid osteoma is a relatively common benign skeletal tumor. The traditional standard treatment has been surgical resection of the nidus. Recently, computed tomography (CT)-guided radiofrequency ablation (RFA) has gained favor as a more precise alternative due to potentially less bone destruction. However, CT-guided RFA is limited in treatment for osteoid osteoma involving complex anatomic structures such as cervical spine, pelvis, or scapula because of difficulty in approach and proximity to neurovascular structures. To solve this problem, we investigated RFA using a new real-time three-dimensional fluoroscopic navigation system. We report its technical procedure and use in a rare case of osteoid osteoma of the scapula.