Entirely intrinsic third ventricular craniopharyngiomas showed characteristics of a round/oval shaped tumor, with rare calcification and cyst formation, and pathologically squamous-papillary type with a positive BRAFV600E mutation. We report an extremely rare case of entirely intrinsic third ventricular craniopharyngioma, pathologically adamantiomatous but with BRAFV600E mutation genetically, developed in a 35-year-old female. It was oval-shaped, with no calcification or cyst, and showed homogeneous enhancement. As shown in this case, it was difficult to differentiate this pathology from chordoid glioma of third ventricle, and the difficulty of this differential diagnosis has not been well documented in previous studies. Our case further implied the importance of molecular diagnosis for subclassification of craniopharyngioma. The BRAFV600E-mutated craniopharyngioma could be the target for the development of treatment with preoperative BRAF-inhibitors. Therefore, differentiation between entirely intrinsic third ventricular craniopharyngiomas and chordoid glioma could be new issue. In this report, we discuss about the preoperative differential diagnosis from chordoid glioma and the literature review. (Received 12 August, 2021; Accepted 21 September, 2021; Published 1 February, 2022).