A 28-year-old man with chondroid chordoma, an uncommon variant of chordoma, is reported. The patient presented with visual disturbance and hypopituitarism. The latter is a rare complication of intracranial chordoma. The preoperative diagnosis of chondroid chordoma of the skull base was based on unique findings on computed tomography and magnetic resonance imaging studies. The development of the tumor over six years suggests that the prognosis of chondroid chordoma may be poor in younger patients, as recently reported. Although chondroid chordoma is very rare, it should be included in the differential diagnosis of hypopituitarism.