The purpose of this study was to compare alveolar bone thickness around the teeth adjacent to the cleft using cone beam computed tomography (CBCT) in patients with cleft lip and palate (CLP) who underwent primary alveolar grafting (PAG) as compared with CLP waiting for secondary alveolar grafting (SAG) and to determine the associations with other factors such as the patient's age, sex, and type of cleft. CBCTs of 39 CLP patients were divided into either group 1 (PAG, N = 11) or group 2 (SAG, N = 28). Measurements of bone thickness around the closest tooth to the cleft were performed on the axial sections on each subject's CBCT at 3, 6, and 9 mm apical to the cementoenamel junction along the root length. Intraclass correlation coefficients and Bland-Altman plots were used to evaluate intrarater reliability. Bone measurements with 95% confidence intervals for the mean were estimated using analysis of variance models with a random patient effect to account for correlation among multiple measurements within a patient. Similar models were used to test the associations of age, sex, and type of the graft with the bone measurements. No statistically significant associations of the factors were found with mesial or distal bone measurements. Buccal bone thickness was significantly greater only at 9 mm in the primary bone graft subjects compared with secondary bone graft subjects (P = 0.009). Unilateral cleft subjects showed significantly greater buccal bone thickness at the level of 9 mm compared with bilateral cleft subjects (P = 0.046) and lingual bone thickness at the level of 6 mm (P = 0.0026) and 9 mm (P = 0.0096). In conclusion, PAG does not add benefits to the bone width on the cleft sides of the closest teeth to the cleft as compared with children with CLP who have not undergone alveolar grafts yet.