Cleidocranial dysplasia is characterized by hypoplasia of the clavicles, unerupted teeth, narrow pelvis, short stature, and craniofacial malformations. A cause of this skeletal dysplasia is heterozygous mutations of the runt-related transcription factor 2 gene ( Runx2 ), a master regulator for bone and cartilage development. Chondrosarcoma is a primary malignant bone tumor that is usually treated by wide resection surgery. This report shows a case of a 25-year-old female patient with cleidocranial dysplasia who was affected with chondrosarcoma of the left humerus. We performed wide resection of the tumor and reconstruction of the large bone defect of the humerus using free vascularized fibular grafts. The patient preserved the hand function and activity of daily life as the same level as preoperative condition more than five years after the surgery.