Extra-axial chordomas in the pediatric population are extremely rare and diagnostically challenging; only four cases have been previously reported with ages ranging from 13 to 20 years. We report a primary extra-axial chordoma involving the soft tissue directly dorsal and ulnar to proximal phalanx in the right thumb of a 12-year-old girl who presented with worsening right thumb pain for 1.5 years. The diagnosis was confirmed by excisional biopsy demonstrating proliferation of large, polygonal epithelioid cells with diffuse expression of pan-cytokeratin and brachyury. The patient required repeat excision for local recurrence seven months later. Since then, she has remained disease free through 15 months surveillance. Extra-axial chordomas share the same histopathological and immunohistochemical characteristics with their axial counterparts and should be considered in the differential diagnosis for any extra-axial bone or soft tissue mass with epithelioid morphology.