Background Gastric fundoplication is the most common noncardiac operation in children with congenital cardiac disease. While prior studies validated safety of laparoscopy in this population, we hypothesize that children with cardiac risk factors (CRFs) are likelier to undergo open fundoplication (OF) but experience greater morbidity than after laparoscopic fundoplication (LF). Materials and methods Utilizing 2013 National Surgical Quality Improvement Program-Pediatrics Public-Use-File, pediatric patients undergoing LF and OF were stratified to none, minor, major, or severe CRFs. Multivariate logistic regression determined preoperative variables and postoperative outcomes associated with LF or OF. Results A total of 1501 fundoplication patients were identified with 92% undergoing LF. OF patients were likelier to have minor (odds ratio [OR]: 2.36, P < 0.001), major (OR: 2.41, P = 0.003), and severe CRFs (OR: 4.36, P < 0.001). Children ≤ 1 y (OR: 3.38, P = 0.048) and those with tracheostomy were likelier to have OF (OR: 2.3, P = 0.006). Overall, the OF group had higher postoperative morbidity (OR: 2.41, P < 0.001). Specifically, children with minor or major CRFs experienced more complications following OF compared to LF. Conclusions OF is more common in patients ≤1 y old; patients with minor, major, or severe CRFs; and those with tracheostomy. LF should be considered in children with minor and major CRFs, as OF in those patients results in greater pulmonary, infectious, and hematological sequelae.