Objective To evaluate factors affecting incidence of complications after secondary alveolar bone grafting with premaxillary osteotomy (SABG + PO) in children with complete bilateral cleft of lip and palate (BCLP). Materials and methods Data were collected from children with BCLP treated with SABG + PO from 2004 to 2014 at our institute. Preoperative parameters included age, donor site, race, gingival health, bone quality around cleft-related teeth, premaxilla position, graft timing, presence of canines in the cleft, and presence of deciduous teeth around the cleft area. Logistic regression and the chi-squared test were used to assess correlations and the incidence of complications. Results In the 64 patients, a significant correlation was found between complication rate and timing of bone grafting with respect to early versus late SABG + PO (p = 0.041), age > 12 years (p = 0.011; odds ratio (OR) 5.9; 95% confidence interval (CI) 1.49-23.93), malposition of the premaxilla (p = 0.042; OR 3.3; 95% CI 1.04-10.13), and preoperative bone quality around cleft-related teeth (p = 0.005; OR 5.3; 95% CI 1.6-17.2). Conclusions The timing of SABG + PO is essential, as early SABG + PO is associated with fewer complications. A malpositioned premaxilla and poor bone quality around cleft-related teeth are associated with more complications. Therefore, preoperative orthodontic repositioning of the malpositioned premaxilla before SABG + PO should be considered. Clinical relevance Analysis of treatment protocols and complications for BCLP patients underscores that proper timing of SABG + PO and correct premaxilla repositioning help reduce complications.