Chordoma is a very rare malignant tumor, with a phenotype that recapitulates notochord, and is chiefly located in the axial skeleton with only few cases reported in the extra-axial skeleton and soft tissues. The diagnosis can be challenging for both clinicians, radiologists and pathologists because of the rarity of tumor, its unspecific radiological pattern and histomorphological similarities to other tumors like extra-skeletal myxoid chondrosarcoma, soft tissue myoepithelioma and metastatic adenocarcinomas, more so on small biopsies. We present a case of a recurrent extra-axial chordoma with a prominent soft tissue component in the left thumb around proximal phalanx of an 80-year-old man, with detailed report of the histopathological, imaging and most importantly molecular features, which are in conformity with the typical profile of notochordal neoplasms. To the best of our knowledge, we report the first DNA-methylation- and the copy number variation analysis of an extra-axial chordoma with a very rare localization, thumb. With this case study we try to give a better understanding of tumor's specification, lessen the diagnostic confusion by highlighting its extra-axial occurrence, and more importantly present substantial molecular data, which might help in providing more therapeutic opportunities in the future.