Premature closure of cranial base synchondroses has been proposed as the mechanism for brachycephaly in dogs and caudal occipital malformation syndrome (COMS) in Cavalier King Charles Spaniels. The purpose of this retrospective study was to compare times of closure for cranial base synchondroses in mesaticephalic, brachycephalic, and Cavalier King Charles Spaniel dogs. Cranial magnetic resonance imaging studies were retrieved for client-owned dogs less than 18 months of age. Breed, age, skull conformation, and the open or closed state of cranial base synchondroses were independently recorded by two observers. For dogs with a unanimous observer agreement, regression analysis was used to test effects of age and gender on the open or closed status of synchondroses and differences between groups. A total of 174 dogs were included in MRI interpretations and 165 dogs were included in the regression analysis. Statistically significant differences in closure time of the spheno-occipital synchondrosis were identified between brachycephalic and mesaticephalic dogs (P = 0.016), Cavalier King Charles Spaniels and mesaticephalic dogs (P < 0.0001), and Cavalier King Charles Spaniels and brachycephalic dogs (P = 0.014). Findings from the current study supported the theory that morphological changes leading to the skull phenotype of the Cavalier King Charles Spaniels could be due to an earlier closure of the spheno-occipital synchondrosis.