Objective Evaluate impact of single-stage versus staged palate repair on the risk of developing malocclusion among patients with cleft palate (CP). Design Retrospective cohort study 2000–2016 Setting Academic, tertiary children’s hospital. Patients Patients undergoing CP repair between 1999–2015. Interventions CP repair, categorized as either single-stage or staged. Main Outcome Measure Time to development of Class III malocclusion. Results 967 patients were included; 60.1% had a two-stage CP repair, and 39.9% had single-stage. Malocclusion was diagnosed in 28.2% of patients. In the model examining all patients at ≤5 years ( n = 659), patients who were not white had a higher risk of malocclusion (HR 2.46, p = 0.004) and staged repair was not protective against malocclusion (HR 0.98, p = 0.91). In all patients >5 years ( n = 411), higher Veau classification and more recent year of birth were significantly associated with higher hazard rates ( p < 0.05). Two-staged repair was not protective against developing malocclusion (HR 0.86, p = 0.60). In the model examining patients with staged repair ≤5 years old ( n = 414), higher age at hard palate closure was associated with reduced malocclusion risk (HR 0.67, p < 0.001) and patients who were not white had increased risk (HR 2.56, p = 0.01). In patients with staged repair >5 years old, more recent birth year may be associated with a higher risk of malocclusion (HR 1.06, p = 0.06) while syndrome may be associated with lower risk of malocclusion diagnosis (HR 0.46, p = 0.07). Conclusion Our data suggests that staged CP repair is not protective against developing Class III malocclusion.