Objective To probe the pathogenesis of long bone defects and damage to epiphysis as the result of postoperative infections following fractures in the childhood of patients, and to look for ideal ways to prevent and repair the defects and damages. Methods The treatment of the infected bone defect of a tibia had been continued for one year following fracture in one four-year old patient, and the treatment of the infected bone defect of a humerus had been continued for ten years following fracture in another seven-year old patient, but all the treatments had failed. The injured limbs developed bone infection, bone defect, bone exposure, shortening, and pseudoarthrosis deformities at last. Then the lesions were completely cleaned, and the deformities of the infected bones were corrected in one stage, with reconstruction of the bone and the repair of the wounds by transplantations of fibular free flaps. Results Both fibular free flaps survived in one stage transplantation. The bones of the injured limbs healed half a year after the operations, and weight-bearing and walking functions of the injured limbs recovered as well. Conclusion Transplantation of fibular free flap was an ideal way to treat a long bone defect as a result of postoperative infection following fracture in the childhood. The early appropriate treatment of postoperative infection following fracture is very important to avoid bone and epiphysis damages.