The spheno-occipital synchondrosis (SOS) is a critical component of midfacial and cranial base growth. Premature closure has been associated with midface hypoplasia in animal models and syndromic craniosynostosis subpopulations with Apert and Muenke syndromes. To link premature SOS closure and midface hypoplasia in patients with Pfeiffer syndrome, a retrospective case-control study was performed in patients treated at a large craniofacial center between 1982 and 2012 diagnosed with Pfeiffer syndrome. At least 1 computed tomography (CT) scan was required to assess SOS patency. Age-/sex-matched control CT scans were also assessed for SOS patency. Three independent reviewers with high interrater reliability (κ = 0.88) graded SOS patency as open, partially closed, or completely closed. Wilcoxon rank sum test compared the Pfeiffer patients with control subjects. A total of 63 CT scans in 16 patients with Pfeiffer syndrome, all with midface hypoplasia, and 63 age-/sex-matched control scans, none of whom had midface hypoplasia, met inclusion criteria. Earliest partial SOS closure in patients with Pfeiffer syndrome was seen at 5 days compared with control subjects at 7.07 years. Earliest age at complete fusion was 2.76 years in the Pfeiffer cohort and 12.74 years in control subjects. Average age at partial closure was significantly younger (4.99 ± 3.33 years; n = 31 scans) in patients with Pfeiffer syndrome compared with control subjects (10.92 ± 3.53 years) (P = 0.0005), whereas average age at complete closure (11.90 ± 7.04 years) was not significantly different than that in control subjects (16.07 ± 3.39 years). Although definitive causality cannot be concluded, a strong correlation exists between midface hypoplasia and premature SOS closure in Pfeiffer syndrome.