In spondyloepiphyseal dysplasia congenita (SEDC), since the cartilage is congenitally abnormal, functional recovery of an intra-articular fracture is uncertain even with surgical treatment. We report a 29-year-old Japanese woman with SEDC whose left knee injury (intercondylar femur fracture and tibial plateau fracture) was surgically reduced and fixed. Although special care was required during the operation for associated atlantoaxial instability and cardiopulmonary suppression due to severe thoracolumbar kyphoscoliosis as well as osteopenia, she had neither restriction of knee motion nor pain at follow-up 2 years and 4 months after surgery. Therefore, although the situation involving fractures in a patient with SEDC is complicated, we believe the main problem to be solved is whether the risk-related kyphoscoliosis and atlantoaxial instability can be managed or not. Fractures themselves can be treated based on the principles used for patients without SEDC.