Background: This study investigates the relationship between paternal and maternal age, and the severity of orofacial clefts and the presence of de novo mutations in children. Methods: This was a retrospective study of individuals who were diagnosed with non-syndromic cleft lip and/or palate (CL/P) and their unaffected parents, from 2012 to 2019. We obtained data from the AfriCRAN project database for Nigerians with non-syndromic orofacial clefts. These individuals were recruited at the Oral and Maxillofacial Surgery Clinic, Lagos University Teaching Hospital, Lagos. Results: There was no statistically significant association between type of CL ± P and parental age in young fathers (p = 0.93). When older fathers were considered, the percentage of complete (more severe) CL ± P cases increased, especially when they were married to older mothers, and this was statistically significant (p = 0.036). In older fathers, the risk of CL ± P in their offspring was increased (OR: 2.66, CI: 1.04-6.80), and there was also an increased risk of developing right-sided CL ± P (OR: 1.61, CI: 1.0-2.59). There was a reduced risk of isolated clefts of the soft palate in younger fathers (OR: 0.36, CI: 0.07–1.71), but the risk increased when considering complete types (more severe) of isolated clefts of the hard and soft palates (OR: 1.63, CI: 0.7–1.7). There was an increase in de novo mutation in children as the difference between paternal and maternal age increased. Conclusion: The study showed that a higher risk of CL ± P and de novo mutations in children is associated with increased parental age.