This study aimed to analyze multicenter patterns in cleft deformity surgeries and identify factors associated with the timing of primary cleft repair in Nigeria. A cross-sectional study of children managed for clefts from January 2009 to December 2020 at three Smile Train partner tertiary institutions situated in the east (Enugu), west (Ibadan), and northern (Jos) parts of the country using a prospectively collected database. Outcomes were the types of surgery performed, yearly volume of surgeries, methods of repair, and time of surgery (early versus late). Of 1043 cleft surgeries, nearly half (45.7%) involved infants (<12 months). Primary repairs of the lip or palate were performed in 83.4% of cases, with 58.4% for lip repairs and 25.1% for palate repairs. The most common cleft lip repair method was a variant of Millard rotation advancement flap. Over the study years, there was a shift from von Langenbeck palatoplasty to methods such as Bardach's palatoplasty and intravelar veloplasty. Patients with bilateral cleft lip defects were significantly more likely (P < 0.001) to undergo early repairs compared with those with unilateral defects. Late primary cleft lip repairs were significantly (P < 0.001) more common in Enugu. This study highlights the variability in cleft surgery patterns in Nigeria. Late primary cleft surgeries were associated with less severe cleft lip or cleft palate and were more prevalent in Enugu, Southeastern Nigeria. The findings contribute valuable insights for optimizing surgical approaches and resource allocation in the management of cleft deformities in the region.