Clinical, radiological, and pathologic features of an intracranial chondroid chordoma in a 9-year-old boy are described. This is the first reported case of a chordoma, the center of which was laterally situated in the cranial base, lying in or near jugular foramen and carotid canal, but without midline involvement. Although cranial chordomas in childhood are extremely rare, and all previously reported cases appeared to have arisen in the clivus, this location should not be considered ectopic. Forking at the rostral end of the notochord has been demonstrated in embryos, and would be the presumed embryological source for this tumor. This is also the first reported case of a chondroid chordoma in a child with immunohistochemical documentation distinguishing it from a chondrosarcoma. This chondroid chordoma contained two populations of cells: neoplastic cartilage and chordoid tissue in a myxoid stroma. The distinction between chordoma and chondrosarcoma and the implications on treatment will be discussed.