Chondromyxoid fibromas are uncommon tumours mostly arising in long bones of young males. Involvement of the skull base is extremely rare. We describe two new cases of base of the skull chondromyxoid fibromas. The tumours were incompletely excised and irradiated with protons because of the high risk of complications of another surgical procedure. The rationale for proton therapy was based on the intimate relations between the tumour and the organs at risk. Skull base chondromyxoid fibroma is a very rare, slowly growing benign tumour that can cause severe disabilities due to tumour compression of critical structures. Only surgical resection has been shown to be relatively effective. We report two cases of incompletely excised lesions treated by postoperative high-dose radiation including proton therapy with no active disease and complication. Our review of the literature allows us to conclude that histological diagnosis of lesions in this site is a trap for pathologists and that radiotherapy is not contraindicated.