Cleidocranial dysplasia (CCD, MIM 119600) is a rare autosomal dominant disorder affecting bone, cartilage, craniofacial growth, and tooth formation leading to supernumerary teeth. Few reports delineate the genotype-phenotype correlations related to the variations in craniofacial morphology and patterning of the dentition and the complexity of treating patient's malocclusion. Successful management of the craniofacial deformities in patients with CCD requires a multidisciplinary team of healthcare specialists. Approximately 70% of patients are due to point mutations in RUNX2 and <20% due to copy number variations with the remainder unidentified. There is no literature to date, describing the orthognathic management of CCD patients with deletion in one of the RUNX2 alleles. The purpose of this study was to evaluate the craniofacial morphology and dental patterning in a 14-year-old Caucasian female with CCD resulting from a novel microdeletion of RUNX2 in 1 allele. The CCD patient with RUNX2 haploinsufficiency due to microdeletion had decreased craniofacial bone and ankyloses in the permanent dentition. An altered extraction protocol of supernumerary teeth was followed in this patient. Craniofacial growth and morphologic analysis demonstrated atypical skull shape, persistent metopic suture, and decreased mandibular size.