The purpose of this paper was to describe the clinical case of a 12-year-old female patient with Klippel-Feil syndrome (KFS) combined with Turner syndrome (TS) and a submucous cleft palate (CP). The patient's general appearance was characterized by KFS, a clinical triad consisting of congenital fusion of at least 2 of 7 cervical vertebrae with a short neck, limited head motion, and a low posterior hairline. Three-dimensional images from cone-beam computed tomography (CBCT) revealed cervical vertebrae anomalies and submucous CP. It was reported that the patient had TS and has been administered growth hormone (GH) therapy. Due to a skeletal class III pattern with a steep mandibular plane angle, facial asymmetry, and fused cervical vertebrae, GH's effects on the craniofacial complex should be considered before orthopedic/orthodontic treatment is started.