Chordoma is a rare bone malignancy that influences the spine and cranium base. Once in a while, it includes bone and when it does, cranial bones are the favored location. Chordomas emerge from embryonic remnants of the primitive notochord and chondrosarcomas from primitive mesenchymal cells, otherwise from the embryonic rest of the cranial cartilaginous matrix. Chondrosarcomas constitute a heterogeneous group of essential bone malignancy characterized by hyaline cartilaginous neoplastic tissue. Both are characterized by invasion and pulverization of the neighboring bone and delicate tissue with higher locoregional reappearance frequency. Chordoma and chondrosarcoma, especially myxoid variation of chondrosarcoma of the cranium base, are as often as possible amalgamated because of similar anatomic location, clinical presentation, and radiologic sightings, and mixed up histopathological highlights. Chordoma and chondrosarcoma vary with respect to their origin, management strategy, and contrast particularly with respect to outcome. Ultimately, developing indication supports aberrant growth factor signaling as possible pathogenic mechanisms in chordoma. Here, we have shown such a location-based symptomatic predicament, understood effectively with ancillary immunohistochemistry. In this review, we summarize the most recent research findings and focus primarily on the pathophysiology and diagnostic aspects.