A 33-year-old female presented with a rare synovial sarcoma manifesting as a painful 12 x 15 mm tumor in the median palmar carpus. Preoperative neurological examination detected only radiating spontaneous pain in her right radial palm and decreased right grasping power. Magnetic resonance (MR) imaging confirmed the presence of the tumor. The preoperative diagnosis was schwannoma originating from the right median nerve. Subcapsular removal of the tumor was performed for preservation of the nerve function. However, postoperative histological and immunohistochemical studies suggested synovial sarcoma originating from the median nerve. No systemic metastasis was detected and the residual tumor capsule was totally removed. Local radiation therapy of 40 Gy, 2 Gy per day, was administered. Fourteen months later, local recurrence was detected on MR imaging. Total removal of the recurrent tumor was performed. Synovial sarcoma was finally diagnosed by the identification of SYT-SSX1 fusion gene transcripts using reverse transcriptase-polymerase chain reaction with a frozen tumor tissue sample.