The National Surgical Quality Improvement Program (NSQIP) Pediatric database has been used to identify factors related to adverse surgical outcomes in pediatric and craniofacial surgical procedures. Focusing on a historically "higher-risk" population, our aim was to assess the impact of demographics, comorbidities, and 22q11.2 deletion syndrome (22QDS) diagnosis on 30-day postoperative complications in patients undergoing primary palatoplasty. We used the 2012-2020 NSQIP Pediatric database to identify patients ≤3 years with and without 22q11.2 deletion syndrome who underwent primary palatoplasty. Demographics, comorbidities, and perioperative characteristics were compared between those with and without 22QDS. Logistic regression was used to determine if children with 22QDS were more likely to experience a 30-day postoperative complication or readmission. There were 10,745 patients ≤3 years old who underwent primary palatoplasty; 83 (0.8%) of whom had 22QDS and 10,662 (99.8%) did not. Children with 22QDS were older when they underwent primary palatoplasty and more likely to have comorbidities. A total of 513 patients (4.8%) experienced a postoperative complication within 30 days and 255 were readmitted (2.4%). Of the 513, 8 (9.6%) had a 22QDS diagnosis and 505 (4.7%) did not. A diagnosis of 22QDS was not a significant independent risk factor for a complication (adjusted odds ratio (aOR) = 1.13; 95% confidence interval (CI): 0.50-2.54) or readmission (aOR = 1.74; 95% CI: 0.74-4.13) within 30 days. This study found that the diagnosis of 22QDS was not an independent predictor of post-palatoplasty complication risk, and in fact 30-day complications are rare for those patients undergoing cleft palate repair, even among those patients with 22QDS.