Introduction: The spheno-occipital synchondrosis (SOS) is a center of endochondral growth that has a late ossification influencing the height and depth of the upper face. Objetive: This study aimed to evaluate the chronological age of complete ossification of the SOS in patients with cleft lip and palate (CLP) and a control group, using cone beam computed tomography (CBCT) images. Materials and methods: The study enrolled 125 patients divided in a CLP group (n = 91) and a control group (n = 34). The SOS of each patient was observed in a CBCT scan and the fusion stage assessed. A chi-square test was used to compare age. A Kaplan-Meyer analysis was used to determine the median time to reach complete ossification of the SOS (p 0.05). Results and Discussion: The experimental group showed statistically significant differences in the median time for complete ossification between males and females (p = 0.019). No statistically significant differences were found in the control group between males and females (p = 0.104). The median time for complete ossification of the SOS was, for males, 15.0 yr in both groups. For females, it was 14.0 yr in the experimental group and 13.0 yr in the control group. Conclusion: The present study showed no differences in the ossification of the SOS between individuals with and without CLP. The complete ossification of this synchondrosis occurs earlier in females than in males. Keywords: cleft lip and palate, spheno-occipital synchondrosis, cranial base, cone beam computed tomography