Primary extra-axial chordomas have been rarely documented, especially in the appendicular bones. Until now, nine such cases, objectively confirmed with positive brachyury immunostaining, have been reported. A 42-year-old male presented with pain in his right tibial tuberosity (shin) of 2–3 years duration without any associated swelling. He denied complaints related to any other lesion elsewhere in his body. Plain radiograph of his lower limbs revealed a large, eccentric, well-defined, lytic lesion containing internal septae with a narrow zone of transition and a sclerotic medullary border in the upper metaphysis of his right tibia, associated with a pathological fracture. There was no other lesion identified in his spine on radiographic imaging. Biopsy sections revealed a tumour composed of polygonal cells with moderate to abundant eosinophilic to vacuolated/‘bubbly’ cytoplasm (physaliphorous cells) arranged in lobules within a conspicuous myxoid matrix. By immunohistochemistry, tumour cells were diffusely positive for pan cytokeratin (AE1/AE3), epithelial membrane antigen (EMA), CK19, S100P, meso (HBME1) and Brachyury/T. Diagnosis of an a primary extra-axial chordoma was finally rendered. Subsequently, the patient underwent bone grafting from his iliac crest. The present case constitutes as the 11th documented case of an extra-axial, intraosseous chordoma and the 10th such case occurring in the appendicular bones. Literature review of similar cases; their diagnostic mimics along with diagnostic and therapeutic implications of such cases are discussed herewith.