Background: Cleft lip and palate are the fourth most common congenital facial anomalies worldwide. Cleft patients have a higher prevalence of dental anomalies than the general population. This study aimed to evaluate the prevalence of hypodontia and supernumerary teeth among the permanent teeth of pediatric patients with clefts at Hospital Pakar Universiti Sains Malaysia (USM). Methods: A retrospective record review study was conducted using dental records and panoramic radiographs from 64 non-syndromic cleft patients aged 6 to 17 years who attended Hospital Pakar USM between 2019 and 2024. Inter-examiner reliability for the assessment of hypodontia was strong, with Cohen’s kappa of 0.89 (95% CI: 0.80-0.98). Statistical analysis was performed using the chi-square and Fisher's exact test (p ≤ 0.05). Results: The prevalence of hypodontia in cleft patients is 90.6% (58 out of 64). Among the total sample, 53.1% (34 out of 64) were patients with UCLP and hypodontia, representing the largest subgroup. The relationship between hypodontia and cleft type is significant (p = 0.005). Among 34 unilateral cleft lip and palate patients, 70.5% (24 out of 34) exhibited hypodontia on both sides; 20.5% (7 out of 34) on the ipsilateral, and 9% (3 out of 34) on the contralateral sides. The relationship between hypodontia and the cleft side is significant (p < 0.001). However, no supernumerary teeth were reported among the 64 cleft patients. Conclusions: Within this single-center retrospective sample, there was a significant association between hypodontia and cleft type and cleft side. These findings underscore the critical importance of early multidisciplinary orthodontic and pediatric dental screening. Hence, larger multicenter studies are needed to confirm these findings.