22q11.2 deletion syndrome (22q11) and trisomy 21 (T21) are frequently associated with tetralogy of Fallot (TOF). We hypothesized that there are differences in postoperative length of stay (LOS) and occurrence of postoperative interventions after complete repair of TOF when comparing children with 22q11 to those with T21. Using the Pediatric Health Information System, we performed a retrospective cohort study of patients who underwent complete repair of TOF from 2004 to 2019. Three groups were identified: 22q11, T21, and controls (those without a coded genetic syndrome). Outcomes were postoperative LOS and composite occurrence (yes/no) of at least one postoperative intervention. Bivariate and multivariate comparisons were made among groups; odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using the control group as the comparator. There were 6924 subjects (n = 493 22q11, n = 455 T21, n = 5976 controls). In bivariate analysis, 22q11 was associated with a longer LOS compared to T21 (OR 2.37 [2.16, 2.60] vs. 1.25 [1.12, 1.39], p 0.001), and 22q11 more often underwent postoperative intervention (OR 3.42 [CI 2.56, 4.57] vs. 1.38 [CI 0.91, 2.11]; p 0.001). In multivariate analysis, 22q11 was also associated with longer LOS (adjusted OR 1.35 [1.26, 1.44] vs. 1.12 [1.04, 1.20]; p 0.001), but there was no difference in the adjusted odds of postoperative intervention. Children with 22q11 are more likely to experience adverse outcomes after repair of TOF compared to those with T21; the differences are most pronounced for LOS.