Truncus arteriosus repair is associated with higher morbidity and mortality compared with many other congenital heart operations. We sought to determine factors associated with mortality and adverse outcomes in infants undergoing truncus arteriosus repair. We used the Pediatric Health Information System Database to identify infants aged < 90 days who underwent truncus arteriosus repair from 2004 to 2019. The primary outcome was hospital mortality. Secondary outcomes were prolonged postoperative length of stay (>30 days) and hospital readmission within 90 days. Multivariable logistic regression models were used to identify associated factors for adverse outcomes. A total of 1645 subjects were included. Hospital mortality occurred in 164 (10%). Factors independently associated with mortality included birth weight < 3 kg, admit age < 48 hours, truncal valve surgery, cardiac arrest, extracorporeal membrane oxygenation, acute kidney injury, cardiac catheterization, tracheostomy, and earlier era. Prolonged postoperative length of stay occurred in 508 patients (31%). Factors independently associated with prolonged postoperative length of stay included prematurity, DiGeorge syndrome, admit age < 48 hours, later surgical era, acute kidney injury, infection, cardiac catheterization, vocal cord paralysis, tracheostomy, and gastrostomy. Readmission within 90 days occurred in 511 of 1481 surviving patients (34%). DiGeorge syndrome, cleft lip/palate, cardiac catheterization, and extracorporeal membrane oxygenation were factors independently associated with hospital readmission. We identified multiple factors associated with hospital mortality and adverse outcomes in infants undergoing truncus arteriosus repair. This information is useful for quality improvement initiatives, perioperative counseling, and discharge planning.