Background: Chondroblastoma is a primary bone tumor typically arising from the intramedullary space of the epiphysis or epimetaphysis. A non-epiphyseal chondroblastoma is uncommon. Case report: An 11-year-old girl presented with an eccentric cortical osteolytic lesion in the distal femur metaphysis. The typical morphology, diffuse H3.3 K36M immunohistochemical expression and H3F3B point mutation (c. 110A > T) unequivocally supported the diagnosis of chondroblastoma. Discussion: We described a non-epiphyseal cortical-based chondroblastoma involving the distal femur harboring the typical H3F3B mutation. Non-epiphyseal chondroblastoma may harbor the H3F3B mutation.