The whistling face syndrome has been reported, with complications of the respiratory system and feeding problems due to microstomia, since 1938. Dysphagia, however, has not previously been reported as a complication of whistling face syndrome. We report a 13-year-old with the whistling face syndrome and dysphagia of late onset who has the typical whistling face, scoliosis and multiple joint contractures. Dysphagia occurred as a result of compression at the cervicomedullary junction by a cranio-vertebral junction malformation and impingement by the tip of the odontoid process. This child had undergone multiple surgical procedures for cleft palate, clubfeet, contractures of the hip and knee and scoliosis. Halo traction and posterior occipital-cervical decompression and fusion successfully treated the dysphagia.