Background: In patients with cleft lip and palate (CLP), secondary alveolar bone grafting (SABG) with particulate cancellous bone marrow (PCBM) is recommended. Objective: To compare bone graft outcomes in patients with unilateral CLP, when SABG is completed before or after canine tooth eruption (ACE or BCE), as measured by cone beam computed tomography (CBCT). Methods: Patients were allocated into two cohorts, ACE and BCE. The outcomes were evaluated using CBCT, followed by univariate and multifactorial analyses. Results: A total of 468 patients (age 11.61 ± 4.03 years; male/female 288/180) were analyzed, including 282 in the BCE group (9.41 ± 1.59 years, 175/107) and 186 in the ACE group (14.95 ± 4.31 years, 113/73). Although 5-level assessment revealed no significant difference in clinical success rate (>4 points) between the BCE and ACE groups (53.90% vs. 47.85%, p = 0.20), BCE group showed significantly higher rate of bone bridges formation (73.05% vs. 62.90%, p = 0.02), which can be attributed to variations in orthodontic participation and follow-up time. Independent predictors of graft failure were wide cleft, severe oronasal fistula, no palatal bone wall, and insufficient PCBM filling (p < 0.01). Conclusions: SABG should be performed before canine eruption with more aggressive PCBM filling and oral fistula management.